Modules

Module

Bases: ABC

Module base class.

Modules are everything that can be passed to jx.integrate, i.e. compartments, branches, cells, and networks.

This base class defines the scaffold for all jaxley modules (compartments, branches, cells, networks).

Source code in jaxley/modules/base.py

class Module(ABC):
    """Module base class.

    Modules are everything that can be passed to `jx.integrate`, i.e. compartments,
    branches, cells, and networks.

    This base class defines the scaffold for all jaxley modules (compartments,
    branches, cells, networks).
    """

    def __init__(self):
        self.nseg: int = None
        self.total_nbranches: int = 0
        self.nbranches_per_cell: List[int] = None

        self.group_nodes = {}

        self.nodes: Optional[pd.DataFrame] = None

        self.edges = pd.DataFrame(
            columns=[
                "pre_locs",
                "pre_branch_index",
                "pre_cell_index",
                "post_locs",
                "post_branch_index",
                "post_cell_index",
                "type",
                "type_ind",
                "global_pre_comp_index",
                "global_post_comp_index",
                "global_pre_branch_index",
                "global_post_branch_index",
            ]
        )

        self.cumsum_nbranches: Optional[jnp.ndarray] = None

        self.comb_parents: jnp.ndarray = jnp.asarray([-1])
        self.comb_branches_in_each_level: List[jnp.ndarray] = [jnp.asarray([0])]

        self.initialized_morph: bool = False
        self.initialized_syns: bool = False

        # List of all types of `jx.Synapse`s.
        self.synapses: List = []
        self.synapse_param_names = []
        self.synapse_state_names = []
        self.synapse_names = []

        # List of types of all `jx.Channel`s.
        self.channels: List[Channel] = []
        self.membrane_current_names: List[str] = []

        # For trainable parameters.
        self.indices_set_by_trainables: List[jnp.ndarray] = []
        self.trainable_params: List[Dict[str, jnp.ndarray]] = []
        self.allow_make_trainable: bool = True
        self.num_trainable_params: int = 0

        # For recordings.
        self.recordings: pd.DataFrame = pd.DataFrame().from_dict({})

        # For stimuli or clamps.
        # E.g. `self.externals = {"v": zeros(1000,2), "i": ones(1000, 2)}`
        # for 1000 timesteps and two compartments.
        self.externals: Dict[str, jnp.ndarray] = {}
        # E.g. `self.external)inds = {"v": jnp.asarray([0,1]), "i": jnp.asarray([2,3])}`
        self.external_inds: Dict[str, jnp.ndarray] = {}

        # x, y, z coordinates and radius.
        self.xyzr: List[np.ndarray] = []

        # For debugging the solver. Will be empty by default and only filled if
        # `self._init_morph_for_debugging` is run.
        self.debug_states = {}

    def _update_nodes_with_xyz(self):
        """Add xyz coordinates to nodes."""
        num_branches = len(self.xyzr)
        x = np.linspace(
            0.5 / self.nseg,
            (num_branches * 1 - 0.5 / self.nseg),
            num_branches * self.nseg,
        )
        x += np.arange(num_branches).repeat(
            self.nseg
        )  # add offset to prevent branch loc overlap
        xp = np.hstack(
            [np.linspace(0, 1, x.shape[0]) + 2 * i for i, x in enumerate(self.xyzr)]
        )
        xyz = v_interp(x, xp, np.vstack(self.xyzr)[:, :3])
        idcs = self.nodes["comp_index"]
        self.nodes.loc[idcs, ["x", "y", "z"]] = xyz.T
        return xyz.T

    def __repr__(self):
        return f"{type(self).__name__} with {len(self.channels)} different channels. Use `.show()` for details."

    def __str__(self):
        return f"jx.{type(self).__name__}"

    def __dir__(self):
        base_dir = object.__dir__(self)
        return sorted(base_dir + self.synapse_names + list(self.group_nodes.keys()))

    def _append_params_and_states(self, param_dict: Dict, state_dict: Dict):
        """Insert the default params of the module (e.g. radius, length).

        This is run at `__init__()`. It does not deal with channels.
        """
        for param_name, param_value in param_dict.items():
            self.nodes[param_name] = param_value
        for state_name, state_value in state_dict.items():
            self.nodes[state_name] = state_value

    def _gather_channels_from_constituents(self, constituents: List):
        """Modify `self.channels` and `self.nodes` with channel info from constituents.

        This is run at `__init__()`. It takes all branches of constituents (e.g.
        of all branches when the are assembled into a cell) and adds columns to
        `.nodes` for the relevant channels.
        """
        for module in constituents:
            for channel in module.channels:
                if channel._name not in [c._name for c in self.channels]:
                    self.channels.append(channel)
                if channel.current_name not in self.membrane_current_names:
                    self.membrane_current_names.append(channel.current_name)
        # Setting columns of channel names to `False` instead of `NaN`.
        for channel in self.channels:
            name = channel._name
            self.nodes.loc[self.nodes[name].isna(), name] = False

    def to_jax(self):
        """Move `.nodes` to `.jaxnodes`.

        Before the actual simulation is run (via `jx.integrate`), all parameters of
        the `jx.Module` are stored in `.nodes` (a `pd.DataFrame`). However, for
        simulation, these parameters have to be moved to be `jnp.ndarrays` such that
        they can be processed on GPU/TPU and such that the simulation can be
        differentiated. `.to_jax()` copies the `.nodes` to `.jaxnodes`.
        """
        self.jaxnodes = {}
        for key, value in self.nodes.to_dict(orient="list").items():
            inds = jnp.arange(len(value))
            self.jaxnodes[key] = jnp.asarray(value)[inds]

        # `jaxedges` contains only parameters (no indices).
        # `jaxedges` contains only non-Nan elements. This is unlike the channels where
        # we allow parameter sharing.
        self.jaxedges = {}
        edges = self.edges.to_dict(orient="list")
        for i, synapse in enumerate(self.synapses):
            for key in synapse.synapse_params:
                condition = np.asarray(edges["type_ind"]) == i
                self.jaxedges[key] = jnp.asarray(np.asarray(edges[key])[condition])
            for key in synapse.synapse_states:
                self.jaxedges[key] = jnp.asarray(np.asarray(edges[key])[condition])

    def show(
        self,
        param_names: Optional[Union[str, List[str]]] = None,  # TODO.
        *,
        indices: bool = True,
        params: bool = True,
        states: bool = True,
        channel_names: Optional[List[str]] = None,
    ) -> pd.DataFrame:
        """Print detailed information about the Module or a view of it.

        Args:
            param_names: The names of the parameters to show. If `None`, all parameters
                are shown. NOT YET IMPLEMENTED.
            indices: Whether to show the indices of the compartments.
            params: Whether to show the parameters of the compartments.
            states: Whether to show the states of the compartments.
            channel_names: The names of the channels to show. If `None`, all channels are
                shown.

        Returns:
            A `pd.DataFrame` with the requested information.
        """
        return self._show(
            self.nodes, param_names, indices, params, states, channel_names
        )

    def _show(
        self,
        view: pd.DataFrame,
        param_names: Optional[Union[str, List[str]]] = None,
        indices: bool = True,
        params: bool = True,
        states: bool = True,
        channel_names: Optional[List[str]] = None,
    ):
        """Print detailed information about the entire Module."""
        printable_nodes = deepcopy(view)

        for channel in self.channels:
            name = channel._name
            param_names = list(channel.channel_params.keys())
            state_names = list(channel.channel_states.keys())
            if channel_names is not None and name not in channel_names:
                printable_nodes = printable_nodes.drop(name, axis=1)
                printable_nodes = printable_nodes.drop(param_names, axis=1)
                printable_nodes = printable_nodes.drop(state_names, axis=1)
            else:
                if not params:
                    printable_nodes = printable_nodes.drop(param_names, axis=1)
                if not states:
                    printable_nodes = printable_nodes.drop(state_names, axis=1)

        if not indices:
            for name in ["comp_index", "branch_index", "cell_index"]:
                printable_nodes = printable_nodes.drop(name, axis=1)

        return printable_nodes

    @abstractmethod
    def init_conds(self, params: Dict):
        """Initialize coupling conductances.

        Args:
            params: Conductances and morphology parameters, not yet including
                coupling conductances.
        """
        raise NotImplementedError

    def _append_channel_to_nodes(self, view: pd.DataFrame, channel: "jx.Channel"):
        """Adds channel nodes from constituents to `self.channel_nodes`."""
        name = channel._name

        # Channel does not yet exist in the `jx.Module` at all.
        if name not in [c._name for c in self.channels]:
            self.channels.append(channel)
            self.nodes[name] = False  # Previous columns do not have the new channel.

        if channel.current_name not in self.membrane_current_names:
            self.membrane_current_names.append(channel.current_name)

        # Add a binary column that indicates if a channel is present.
        self.nodes.loc[view.index.values, name] = True

        # Loop over all new parameters, e.g. gNa, eNa.
        for key in channel.channel_params:
            self.nodes.loc[view.index.values, key] = channel.channel_params[key]

        # Loop over all new parameters, e.g. gNa, eNa.
        for key in channel.channel_states:
            self.nodes.loc[view.index.values, key] = channel.channel_states[key]

    def set(self, key: str, val: Union[float, jnp.ndarray]):
        """Set parameter of module (or its view) to a new value.

        Note that this function can not be called within `jax.jit` or `jax.grad`.
        Instead, it should be used set the parameters of the module **before** the
        simulation. Use `.data_set()` to set parameters during `jax.jit` or
        `jax.grad`.

        Args:
            key: The name of the parameter to set.
            val: The value to set the parameter to. If it is `jnp.ndarray` then it
                must be of shape `(len(num_compartments))`.
        """
        # TODO(@michaeldeistler) should we allow `.set()` for synaptic parameters
        # without using the `SynapseView`, purely for consistency with `make_trainable`?
        view = (
            self.edges
            if key in self.synapse_param_names or key in self.synapse_state_names
            else self.nodes
        )
        self._set(key, val, view, view)

    def _set(
        self,
        key: str,
        val: Union[float, jnp.ndarray],
        view: pd.DataFrame,
        table_to_update: pd.DataFrame,
    ):
        if key in view.columns:
            view = view[~np.isnan(view[key])]
            table_to_update.loc[view.index.values, key] = val
        else:
            raise KeyError("Key not recognized.")

    def data_set(
        self,
        key: str,
        val: Union[float, jnp.ndarray],
        param_state: Optional[List[Dict]],
    ):
        """Set parameter of module (or its view) to a new value within `jit`.

        Args:
            key: The name of the parameter to set.
            val: The value to set the parameter to. If it is `jnp.ndarray` then it
                must be of shape `(len(num_compartments))`.
            param_state: State of the setted parameters, internally used such that this
                function does not modify global state.
        """
        view = (
            self.edges
            if key in self.synapse_param_names or key in self.synapse_state_names
            else self.nodes
        )
        return self._data_set(key, val, view, param_state=param_state)

    def _data_set(
        self,
        key: str,
        val: Tuple[float, jnp.ndarray],
        view: pd.DataFrame,
        param_state: Optional[List[Dict]] = None,
    ):
        # Note: `data_set` does not support arrays for `val`.
        if key in view.columns:
            view = view[~np.isnan(view[key])]
            added_param_state = [
                {
                    "indices": np.atleast_2d(view.index.values),
                    "key": key,
                    "val": jnp.atleast_1d(jnp.asarray(val)),
                }
            ]
            if param_state is not None:
                param_state += added_param_state
            else:
                param_state = added_param_state
        else:
            raise KeyError("Key not recognized.")
        return param_state

    def make_trainable(
        self,
        key: str,
        init_val: Optional[Union[float, list]] = None,
        verbose: bool = True,
    ):
        """Make a parameter trainable.

        If a parameter is made trainable, it will be returned by `get_parameters()`
        and should then be passed to `jx.integrate(..., params=params)`.

        Args:
            key: Name of the parameter to make trainable.
            init_val: Initial value of the parameter. If `float`, the same value is
                used for every created parameter. If `list`, the length of the list has
                to match the number of created parameters. If `None`, the current
                parameter value is used and if parameter sharing is performed that the
                current parameter value is averaged over all shared parameters.
            verbose: Whether to print the number of parameters that are added and the
                total number of parameters.
        """
        assert (
            key not in self.synapse_param_names and key not in self.synapse_state_names
        ), "Parameters of synapses can only be made trainable via the `SynapseView`."
        view = self.nodes
        view = deepcopy(view.assign(controlled_by_param=0))
        self._make_trainable(view, key, init_val, verbose=verbose)

    def _make_trainable(
        self,
        view: pd.DataFrame,
        key: str,
        init_val: Optional[Union[float, list]] = None,
        verbose: bool = True,
    ):
        assert (
            self.allow_make_trainable
        ), "network.cell('all').make_trainable() is not supported. Use a for-loop over cells."

        if key in view.columns:
            view = view[~np.isnan(view[key])]
            grouped_view = view.groupby("controlled_by_param")
            # Because of this `x.index.values` we cannot support `make_trainable()` on
            # the module level for synapse parameters (but only for `SynapseView`).
            inds_of_comps = list(grouped_view.apply(lambda x: x.index.values))

            # Sorted inds are only used to infer the correct starting values.
            param_vals = jnp.asarray(
                [view.loc[inds, key].to_numpy() for inds in inds_of_comps]
            )
        else:
            raise KeyError(f"Parameter {key} not recognized.")

        indices_per_param = jnp.stack(inds_of_comps)
        self.indices_set_by_trainables.append(indices_per_param)

        # Set the value which the trainable parameter should take.
        num_created_parameters = len(indices_per_param)
        if init_val is not None:
            if isinstance(init_val, float):
                new_params = jnp.asarray([init_val] * num_created_parameters)
            elif isinstance(init_val, list):
                assert (
                    len(init_val) == num_created_parameters
                ), f"len(init_val)={len(init_val)}, but trying to create {num_created_parameters} parameters."
                new_params = jnp.asarray(init_val)
            else:
                raise ValueError(
                    f"init_val must a float, list, or None, but it is a {type(init_val).__name__}."
                )
        else:
            new_params = jnp.mean(param_vals, axis=1)

        self.trainable_params.append({key: new_params})
        self.num_trainable_params += num_created_parameters
        if verbose:
            print(
                f"Number of newly added trainable parameters: {num_created_parameters}. Total number of trainable parameters: {self.num_trainable_params}"
            )

    def delete_trainables(self):
        """Removes all trainable parameters from the module."""
        self.indices_set_by_trainables: List[jnp.ndarray] = []
        self.trainable_params: List[Dict[str, jnp.ndarray]] = []
        self.num_trainable_params: int = 0

    def add_to_group(self, group_name: str):
        """Add a view of the module to a group.

        Groups can then be indexed. For example:
        ```python
        net.cell(0).add_to_group("excitatory")
        net.excitatory.set("radius", 0.1)
        ```

        Args:
            group_name: The name of the group.
        """
        raise ValueError("`add_to_group()` makes no sense for an entire module.")

    def _add_to_group(self, group_name: str, view: pd.DataFrame):
        if group_name in self.group_nodes:
            view = pd.concat([self.group_nodes[group_name], view])
        self.group_nodes[group_name] = view

    def get_parameters(self) -> List[Dict[str, jnp.ndarray]]:
        """Get all trainable parameters.

        The returned parameters should be passed to `jx.integrate(..., params=params).

        Returns:
            A list of all trainable parameters in the form of
                [{"gNa": jnp.array([0.1, 0.2, 0.3])}, ...].
        """
        return self.trainable_params

    def get_all_parameters(self, pstate: List[Dict]) -> Dict[str, jnp.ndarray]:
        """Return all parameters (and coupling conductances) needed to simulate.

        Runs `init_conds()` and return every parameter that is needed to solve the ODE.
        This includes conductances, radiuses, lengths, axial_resistivities, but also
        coupling conductances.

        This is done by first obtaining the current value of every parameter (not only
        the trainable ones) and then replacing the trainable ones with the value
        in `trainable_params()`. This function is run within `jx.integrate()`.

        pstate can be obtained by calling `params_to_pstate()`.
        ```
        params = module.get_parameters() # i.e. [0, 1, 2]
        pstate = params_to_pstate(params, module.indices_set_by_trainables)
        module.to_jax() # needed for call to module.jaxnodes
        ```

        Args:
            pstate: The state of the trainable parameters. pstate takes the form
                [{"key": "gNa", "indices": jnp.array([0, 1, 2]), "val": jnp.array([0.1, 0.2, 0.3])}, ...].

        Returns:
            A dictionary of all module parameters.
        """
        params = {}
        for key in ["radius", "length", "axial_resistivity", "capacitance"]:
            params[key] = self.jaxnodes[key]

        for channel in self.channels:
            for channel_params in channel.channel_params:
                params[channel_params] = self.jaxnodes[channel_params]

        for synapse_params in self.synapse_param_names:
            params[synapse_params] = self.jaxedges[synapse_params]

        # Override with those parameters set by `.make_trainable()`.
        for parameter in pstate:
            key = parameter["key"]
            inds = parameter["indices"]
            set_param = parameter["val"]
            if key in params:  # Only parameters, not initial states.
                # `inds` is of shape `(num_params, num_comps_per_param)`.
                # `set_param` is of shape `(num_params,)`
                # We need to unsqueeze `set_param` to make it `(num_params, 1)` for the
                # `.set()` to work. This is done with `[:, None]`.
                params[key] = params[key].at[inds].set(set_param[:, None])

        # Compute conductance params and append them.
        cond_params = self.init_conds(params)
        for key in cond_params:
            params[key] = cond_params[key]

        return params

    def get_states_from_nodes_and_edges(self):
        """Return states as they are set in the `.nodes` and `.edges` tables."""
        self.to_jax()  # Create `.jaxnodes` from `.nodes` and `.jaxedges` from `.edges`.
        states = {"v": self.jaxnodes["v"]}
        # Join node and edge states into a single state dictionary.
        for channel in self.channels:
            for channel_states in channel.channel_states:
                states[channel_states] = self.jaxnodes[channel_states]
        for synapse_states in self.synapse_state_names:
            states[synapse_states] = self.jaxedges[synapse_states]
        return states

    def get_all_states(
        self, pstate: List[Dict], all_params, delta_t: float
    ) -> Dict[str, jnp.ndarray]:
        """Get the full initial state of the module from jaxnodes and trainables.

        Args:
            pstate: The state of the trainable parameters.
            all_params: All parameters of the module.
            delta_t: The time step.

        Returns:
            A dictionary of all states of the module.
        """
        states = self.get_states_from_nodes_and_edges()

        # Override with the initial states set by `.make_trainable()`.
        for parameter in pstate:
            key = parameter["key"]
            inds = parameter["indices"]
            set_param = parameter["val"]
            if key in states:  # Only initial states, not parameters.
                # `inds` is of shape `(num_params, num_comps_per_param)`.
                # `set_param` is of shape `(num_params,)`
                # We need to unsqueeze `set_param` to make it `(num_params, 1)` for the
                # `.set()` to work. This is done with `[:, None]`.
                states[key] = states[key].at[inds].set(set_param[:, None])

        # Add to the states the initial current through every channel.
        states, _ = self._channel_currents(
            states, delta_t, self.channels, self.nodes, all_params
        )

        # Add to the states the initial current through every synapse.
        states, _ = self._synapse_currents(
            states, self.synapses, all_params, delta_t, self.edges
        )
        return states

    @property
    def initialized(self):
        """Whether the `Module` is ready to be solved or not."""
        return self.initialized_morph and self.initialized_syns

    def initialize(self):
        """Initialize the module."""
        self.init_morph()
        return self

    def init_states(self, delta_t: float = 0.025):
        """Initialize all mechanisms in their steady state.

        This considers the voltages and parameters of each compartment.

        Args:
            delta_t: Passed on to `channel.init_state()`.
        """
        # Update states of the channels.
        channel_nodes = self.nodes
        states = self.get_states_from_nodes_and_edges()

        # We do not use any `pstate` for initializing. In principle, we could change
        # that by allowing an input `params` and `pstate` to this function.
        params = self.get_all_parameters([])

        for channel in self.channels:
            name = channel._name
            channel_indices = channel_nodes.loc[channel_nodes[name]][
                "comp_index"
            ].to_numpy()
            voltages = channel_nodes.loc[channel_indices, "v"].to_numpy()

            channel_param_names = list(channel.channel_params.keys())
            channel_state_names = list(channel.channel_states.keys())
            channel_states = query_channel_states_and_params(
                states, channel_state_names, channel_indices
            )
            channel_params = query_channel_states_and_params(
                params, channel_param_names, channel_indices
            )

            init_state = channel.init_state(
                channel_states, voltages, channel_params, delta_t
            )

            # `init_state` might not return all channel states. Only the ones that are
            # returned are updated here.
            for key, val in init_state.items():
                # Note that we are overriding `self.nodes` here, but `self.nodes` is
                # not used above to actually compute the current states (so there are
                # no issues with overriding states).
                self.nodes.loc[channel_indices, key] = val

    def _init_morph_for_debugging(self):
        """Instandiates row and column inds which can be used to solve the voltage eqs.

        This is important only for expert users who try to modify the solver for the
        voltage equations. By default, this function is never run.

        This is useful for debugging the solver because one can use
        `scipy.linalg.sparse.spsolve` after every step of the solve.

        Here is the code snippet that can be used for debugging then (to be inserted in
        `solver_voltage`):
        ```python
        from scipy.sparse import csc_matrix
        from scipy.sparse.linalg import spsolve
        from jaxley.utils.debug_solver import build_voltage_matrix_elements

        elements, solve, num_entries, start_ind_for_branchpoints = (
            build_voltage_matrix_elements(
                uppers,
                lowers,
                diags,
                solves,
                branchpoint_conds_children[debug_states["child_inds"]],
                branchpoint_conds_parents[debug_states["par_inds"]],
                branchpoint_weights_children[debug_states["child_inds"]],
                branchpoint_weights_parents[debug_states["par_inds"]],
                branchpoint_diags,
                branchpoint_solves,
                debug_states["nseg"],
                nbranches,
            )
        )
        sparse_matrix = csc_matrix(
            (elements, (debug_states["row_inds"], debug_states["col_inds"])),
            shape=(num_entries, num_entries),
        )
        solution = spsolve(sparse_matrix, solve)
        solution = solution[:start_ind_for_branchpoints]  # Delete branchpoint voltages.
        solves = jnp.reshape(solution, (debug_states["nseg"], nbranches))
        return solves
        ```
        """
        # For scipy and jax.scipy.
        row_and_col_inds = compute_morphology_indices(
            len(self.par_inds),
            self.child_belongs_to_branchpoint,
            self.par_inds,
            self.child_inds,
            self.nseg,
            self.total_nbranches,
        )

        num_elements = len(row_and_col_inds["row_inds"])
        data_inds, indices, indptr = convert_to_csc(
            num_elements=num_elements,
            row_ind=row_and_col_inds["row_inds"],
            col_ind=row_and_col_inds["col_inds"],
        )
        self.debug_states["row_inds"] = row_and_col_inds["row_inds"]
        self.debug_states["col_inds"] = row_and_col_inds["col_inds"]
        self.debug_states["data_inds"] = data_inds
        self.debug_states["indices"] = indices
        self.debug_states["indptr"] = indptr

        self.debug_states["nseg"] = self.nseg
        self.debug_states["child_inds"] = self.child_inds
        self.debug_states["par_inds"] = self.par_inds

    def record(self, state: str = "v", verbose: bool = True):
        """Insert a recording into the compartment.

        Args:
            state: The name of the state to record.
            verbose: Whether to print number of inserted recordings."""
        view = deepcopy(self.nodes)
        view["state"] = state
        recording_view = view[["comp_index", "state"]]
        recording_view = recording_view.rename(columns={"comp_index": "rec_index"})
        self._record(recording_view, verbose=verbose)

    def _record(self, view: pd.DataFrame, verbose: bool = True):
        self.recordings = pd.concat([self.recordings, view], ignore_index=True)
        if verbose:
            print(f"Added {len(view)} recordings. See `.recordings` for details.")

    def delete_recordings(self):
        """Removes all recordings from the module."""
        self.recordings = pd.DataFrame().from_dict({})

    def stimulate(self, current: Optional[jnp.ndarray] = None, verbose: bool = True):
        """Insert a stimulus into the compartment.

        current must be a 1d array or have batch dimension of size `(num_compartments, )`
        or `(1, )`. If 1d, the same stimulus is added to all compartments.

        This function cannot be run during `jax.jit` and `jax.grad`. Because of this,
        it should only be used for static stimuli (i.e., stimuli that do not depend
        on the data and that should not be learned). For stimuli that depend on data
        (or that should be learned), please use `data_stimulate()`.

        Args:
            current: Current in `nA`.
        """
        self._external_input("i", current, self.nodes, verbose=verbose)

    def clamp(self, state_name: str, state_array: jnp.ndarray, verbose: bool = True):
        """Clamp a state to a given value across specified compartments.

        Args:
            state_name: The name of the state to clamp.
            state_array (jnp.nd: Array of values to clamp the state to.
            verbose : If True, prints details about the clamping.

        This function sets external states for the compartments.
        """
        if state_name not in self.nodes.columns:
            raise KeyError(f"{state_name} is not a recognized state in this module.")
        self._external_input(state_name, state_array, self.nodes, verbose=verbose)

    def _external_input(
        self,
        key: str,
        values: Optional[jnp.ndarray],
        view: pd.DataFrame,
        verbose: bool = True,
    ):
        values = values if values.ndim == 2 else jnp.expand_dims(values, axis=0)
        batch_size = values.shape[0]
        is_multiple = len(view) == batch_size
        values = values if is_multiple else jnp.repeat(values, len(view), axis=0)
        assert batch_size in [1, len(view)], "Number of comps and stimuli do not match."

        if key in self.externals.keys():
            self.externals[key] = jnp.concatenate([self.externals[key], values])
            self.external_inds[key] = jnp.concatenate(
                [self.external_inds[key], view.comp_index.to_numpy()]
            )
        else:
            self.externals[key] = values
            self.external_inds[key] = view.comp_index.to_numpy()

        if verbose:
            print(f"Added {len(view)} external_states. See `.externals` for details.")

    def data_stimulate(
        self,
        current: jnp.ndarray,
        data_stimuli: Optional[Tuple[jnp.ndarray, pd.DataFrame]] = None,
        verbose: bool = False,
    ) -> Tuple[jnp.ndarray, pd.DataFrame]:
        """Insert a stimulus into the module within jit (or grad).

        Args:
            current: Current in `nA`.
            verbose: Whether or not to print the number of inserted stimuli. `False`
                by default because this method is meant to be jitted.
        """
        return self._data_stimulate(current, data_stimuli, self.nodes, verbose=verbose)

    def _data_stimulate(
        self,
        current: jnp.ndarray,
        data_stimuli: Optional[Tuple[jnp.ndarray, pd.DataFrame]],
        view: pd.DataFrame,
        verbose: bool = False,
    ) -> Tuple[jnp.ndarray, pd.DataFrame]:
        current = current if current.ndim == 2 else jnp.expand_dims(current, axis=0)
        batch_size = current.shape[0]
        is_multiple = len(view) == batch_size
        current = current if is_multiple else jnp.repeat(current, len(view), axis=0)
        assert batch_size in [1, len(view)], "Number of comps and stimuli do not match."

        if data_stimuli is not None:
            currents = data_stimuli[0]
            inds = data_stimuli[1]
        else:
            currents = None
            inds = pd.DataFrame().from_dict({})

        # Same as in `.stimulate()`.
        if currents is not None:
            currents = jnp.concatenate([currents, current])
        else:
            currents = current
        inds = pd.concat([inds, view])

        if verbose:
            print(f"Added {len(view)} stimuli.")

        return (currents, inds)

    def delete_stimuli(self):
        """Removes all stimuli from the module."""
        self.externals.pop("i", None)
        self.external_inds.pop("i", None)

    def insert(self, channel: Channel):
        """Insert a channel into the module.

        Args:
            channel: The channel to insert."""
        self._insert(channel, self.nodes)

    def _insert(self, channel, view):
        self._append_channel_to_nodes(view, channel)

    def init_syns(self):
        self.initialized_syns = True

    def init_morph(self):
        self.initialized_morph = True

    def step(
        self,
        u: Dict[str, jnp.ndarray],
        delta_t: float,
        external_inds: Dict[str, jnp.ndarray],
        externals: Dict[str, jnp.ndarray],
        params: Dict[str, jnp.ndarray],
        solver: str = "bwd_euler",
        voltage_solver: str = "jaxley.stone",
    ) -> Dict[str, jnp.ndarray]:
        """One step of solving the Ordinary Differential Equation.

        This function is called inside of `integrate` and increments the state of the
        module by one time step. Calls `_step_channels` and `_step_synapse` to update
        the states of the channels and synapses using fwd_euler.

        Args:
            u: The state of the module. voltages = u["v"]
            delta_t: The time step.
            external_inds: The indices of the external inputs.
            externals: The external inputs.
            params: The parameters of the module.
            solver: The solver to use for the voltages. Either of ["bwd_euler",
                "fwd_euler", "crank_nicolson"].
            voltage_solver: The tridiagonal solver used to diagonalize the
                coefficient matrix of the ODE system. Either of ["jaxley.thomas",
                "jaxley.stone"].

        Returns:
            The updated state of the module.
        """

        # Extract the voltages
        voltages = u["v"]

        # Extract the external inputs
        has_current = "i" in externals.keys()
        i_current = externals["i"] if has_current else jnp.asarray([]).astype("float")
        i_inds = external_inds["i"] if has_current else jnp.asarray([]).astype("int32")
        i_ext = self._get_external_input(
            voltages, i_inds, i_current, params["radius"], params["length"]
        )

        # Step of the channels.
        u, (v_terms, const_terms) = self._step_channels(
            u, delta_t, self.channels, self.nodes, params
        )

        # Step of the synapse.
        u, (syn_v_terms, syn_const_terms) = self._step_synapse(
            u,
            self.synapses,
            params,
            delta_t,
            self.edges,
        )

        # Clamp for channels and synapses.
        for key in externals.keys():
            if key not in ["i", "v"]:
                u[key] = u[key].at[external_inds[key]].set(externals[key])

        # Voltage steps.
        cm = params["capacitance"]  # Abbreviation.

        solver_kwargs = {
            "voltages": voltages,
            "voltage_terms": (v_terms + syn_v_terms) / cm,
            "constant_terms": (const_terms + i_ext + syn_const_terms) / cm,
            "coupling_conds_upper": params["branch_uppers"],
            "coupling_conds_lower": params["branch_lowers"],
            "summed_coupling_conds": params["branch_diags"],
            "branchpoint_conds_children": params["branchpoint_conds_children"],
            "branchpoint_conds_parents": params["branchpoint_conds_parents"],
            "branchpoint_weights_children": params["branchpoint_weights_children"],
            "branchpoint_weights_parents": params["branchpoint_weights_parents"],
            "par_inds": self.par_inds,
            "child_inds": self.child_inds,
            "nbranches": self.total_nbranches,
            "solver": voltage_solver,
            "children_in_level": self.children_in_level,
            "parents_in_level": self.parents_in_level,
            "root_inds": self.root_inds,
            "branchpoint_group_inds": self.branchpoint_group_inds,
            "debug_states": self.debug_states,
        }
        if solver == "bwd_euler":
            new_voltages = step_voltage_implicit(**solver_kwargs, delta_t=delta_t)
            u["v"] = new_voltages.ravel(order="C")
        elif solver == "fwd_euler":
            new_voltages = step_voltage_explicit(**solver_kwargs, delta_t=delta_t)
            u["v"] = new_voltages.ravel(order="C")
        elif solver == "crank_nicolson":
            # Crank Nicolson advances by half a step of backward and half a step of
            # forward Euler.
            half_step_delta_t = delta_t / 2
            half_step_voltages = step_voltage_implicit(
                **solver_kwargs, delta_t=half_step_delta_t
            )
            # The forward Euler step in Crank Nicolson can be performed easily as
            # `V_{n+1} = 2 * V_{n+1/2} - V_n`. See also NEURON book Chapter 4.
            u["v"] = 2 * half_step_voltages.ravel(order="C") - voltages
        else:
            raise ValueError(
                f"You specified `solver={solver}`. The only allowed solvers are "
                "['bwd_euler', 'fwd_euler', 'crank_nicolson']."
            )

        # Clamp for voltages.
        if "v" in externals.keys():
            u["v"] = u["v"].at[external_inds["v"]].set(externals["v"])

        return u

    def _step_channels(
        self,
        states: Dict[str, jnp.ndarray],
        delta_t: float,
        channels: List[Channel],
        channel_nodes: pd.DataFrame,
        params: Dict[str, jnp.ndarray],
    ) -> Tuple[Dict[str, jnp.ndarray], Tuple[jnp.ndarray, jnp.ndarray]]:
        """One step of integration of the channels and of computing their current."""
        states = self._step_channels_state(
            states, delta_t, channels, channel_nodes, params
        )
        states, current_terms = self._channel_currents(
            states, delta_t, channels, channel_nodes, params
        )
        return states, current_terms

    def _step_channels_state(
        self,
        states,
        delta_t,
        channels: List[Channel],
        channel_nodes: pd.DataFrame,
        params: Dict[str, jnp.ndarray],
    ) -> Dict[str, jnp.ndarray]:
        """One integration step of the channels."""
        voltages = states["v"]

        # Update states of the channels.
        indices = channel_nodes["comp_index"].to_numpy()
        for channel in channels:
            channel_param_names = list(channel.channel_params)
            channel_param_names += ["radius", "length", "axial_resistivity"]
            channel_state_names = list(channel.channel_states)
            channel_state_names += self.membrane_current_names
            channel_indices = indices[channel_nodes[channel._name].astype(bool)]

            channel_params = query_channel_states_and_params(
                params, channel_param_names, channel_indices
            )
            channel_states = query_channel_states_and_params(
                states, channel_state_names, channel_indices
            )

            states_updated = channel.update_states(
                channel_states, delta_t, voltages[channel_indices], channel_params
            )
            # Rebuild state. This has to be done within the loop over channels to allow
            # multiple channels which modify the same state.
            for key, val in states_updated.items():
                states[key] = states[key].at[channel_indices].set(val)

        return states

    def _channel_currents(
        self,
        states: Dict[str, jnp.ndarray],
        delta_t: float,
        channels: List[Channel],
        channel_nodes: pd.DataFrame,
        params: Dict[str, jnp.ndarray],
    ) -> Tuple[Dict[str, jnp.ndarray], Tuple[jnp.ndarray, jnp.ndarray]]:
        """Return the current through each channel.

        This is also updates `state` because the `state` also contains the current.
        """
        voltages = states["v"]

        # Compute current through channels.
        voltage_terms = jnp.zeros_like(voltages)
        constant_terms = jnp.zeros_like(voltages)
        # Run with two different voltages that are `diff` apart to infer the slope and
        # offset.
        diff = 1e-3

        current_states = {}
        for name in self.membrane_current_names:
            current_states[name] = jnp.zeros_like(voltages)

        for channel in channels:
            name = channel._name
            channel_param_names = list(channel.channel_params.keys())
            channel_state_names = list(channel.channel_states.keys())
            indices = channel_nodes.loc[channel_nodes[name]]["comp_index"].to_numpy()

            channel_params = {}
            for p in channel_param_names:
                channel_params[p] = params[p][indices]
            channel_params["radius"] = params["radius"][indices]
            channel_params["length"] = params["length"][indices]
            channel_params["axial_resistivity"] = params["axial_resistivity"][indices]

            channel_states = {}
            for s in channel_state_names:
                channel_states[s] = states[s][indices]

            v_and_perturbed = jnp.stack([voltages[indices], voltages[indices] + diff])
            membrane_currents = vmap(channel.compute_current, in_axes=(None, 0, None))(
                channel_states, v_and_perturbed, channel_params
            )
            voltage_term = (membrane_currents[1] - membrane_currents[0]) / diff
            constant_term = membrane_currents[0] - voltage_term * voltages[indices]
            voltage_terms = voltage_terms.at[indices].add(voltage_term)
            constant_terms = constant_terms.at[indices].add(-constant_term)

            # Save the current (for the unperturbed voltage) as a state that will
            # also be passed to the state update.
            current_states[channel.current_name] = (
                current_states[channel.current_name]
                .at[indices]
                .add(membrane_currents[0])
            )

        # Copy the currents into the `state` dictionary such that they can be
        # recorded and used by `Channel.update_states()`.
        for name in self.membrane_current_names:
            states[name] = current_states[name]

        return states, (voltage_terms, constant_terms)

    def _step_synapse(
        self,
        u: Dict[str, jnp.ndarray],
        syn_channels: List[Channel],
        params: Dict[str, jnp.ndarray],
        delta_t: float,
        edges: pd.DataFrame,
    ) -> Tuple[Dict[str, jnp.ndarray], Tuple[jnp.ndarray, jnp.ndarray]]:
        """One step of integration of the channels.

        `Network` overrides this method (because it actually has synapses), whereas
        `Compartment`, `Branch`, and `Cell` do not override this.
        """
        voltages = u["v"]
        return u, (jnp.zeros_like(voltages), jnp.zeros_like(voltages))

    def _synapse_currents(
        self, states, syn_channels, params, delta_t, edges: pd.DataFrame
    ) -> Tuple[Dict[str, jnp.ndarray], Tuple[jnp.ndarray, jnp.ndarray]]:
        return states, (None, None)

    @staticmethod
    def _get_external_input(
        voltages: jnp.ndarray,
        i_inds: jnp.ndarray,
        i_stim: jnp.ndarray,
        radius: float,
        length_single_compartment: float,
    ) -> jnp.ndarray:
        """
        Return external input to each compartment in uA / cm^2.

        Args:
            voltages: mV.
            i_stim: nA.
            radius: um.
            length_single_compartment: um.
        """
        zero_vec = jnp.zeros_like(voltages)
        current = convert_point_process_to_distributed(
            i_stim, radius[i_inds], length_single_compartment[i_inds]
        )

        dnums = ScatterDimensionNumbers(
            update_window_dims=(),
            inserted_window_dims=(0,),
            scatter_dims_to_operand_dims=(0,),
        )
        stim_at_timestep = scatter_add(zero_vec, i_inds[:, None], current, dnums)
        return stim_at_timestep

    def vis(
        self,
        ax: Optional[Axes] = None,
        col: str = "k",
        dims: Tuple[int] = (0, 1),
        type: str = "line",
        morph_plot_kwargs: Dict = {},
    ) -> Axes:
        """Visualize the module.

        Args:
            ax: An axis into which to plot.
            col: The color for all branches.
            dims: Which dimensions to plot. 1=x, 2=y, 3=z coordinate. Must be a tuple of
                two of them.
            morph_plot_kwargs: Keyword arguments passed to the plotting function.
        """
        return self._vis(
            dims=dims,
            col=col,
            ax=ax,
            view=self.nodes,
            type=type,
            morph_plot_kwargs=morph_plot_kwargs,
        )

    def _vis(
        self,
        ax: Axes,
        col: str,
        dims: Tuple[int],
        view: pd.DataFrame,
        type: str,
        morph_plot_kwargs: Dict,
    ) -> Axes:
        branches_inds = view["branch_index"].to_numpy()
        coords = []
        for branch_ind in branches_inds:
            assert not np.any(
                np.isnan(self.xyzr[branch_ind][:, dims])
            ), "No coordinates available. Use `vis(detail='point')` or run `.compute_xyz()` before running `.vis()`."
            coords.append(self.xyzr[branch_ind])

        ax = plot_morph(
            coords,
            dims=dims,
            col=col,
            ax=ax,
            type=type,
            morph_plot_kwargs=morph_plot_kwargs,
        )

        return ax

    def _scatter(self, ax, col, dims, view, morph_plot_kwargs):
        """Scatter visualization (used only for compartments)."""
        assert len(view) == 1, "Scatter only deals with compartments."
        branch_ind = view["branch_index"].to_numpy().item()
        comp_ind = view["comp_index"].to_numpy().item()
        assert not np.any(
            np.isnan(self.xyzr[branch_ind][:, dims])
        ), "No coordinates available. Use `vis(detail='point')` or run `.compute_xyz()` before running `.vis()`."

        comp_fraction = loc_of_index(comp_ind, self.nseg)
        coords = self.xyzr[branch_ind]
        interpolated_xyz = interpolate_xyz(comp_fraction, coords)

        ax = plot_morph(
            np.asarray([[interpolated_xyz]]),
            dims=dims,
            col=col,
            ax=ax,
            type="scatter",
            morph_plot_kwargs=morph_plot_kwargs,
        )

        return ax

    def compute_xyz(self):
        """Return xyz coordinates of every branch, based on the branch length.

        This function should not be called if the morphology was read from an `.swc`
        file. However, for morphologies that were constructed from scratch, this
        function **must** be called before `.vis()`. The computed `xyz` coordinates
        are only used for plotting.
        """
        max_y_multiplier = 5.0
        min_y_multiplier = 0.5

        parents = self.comb_parents
        num_children = _compute_num_children(parents)
        index_of_child = _compute_index_of_child(parents)
        levels = compute_levels(parents)

        # Extract branch.
        inds_branch = self.nodes.groupby("branch_index")["comp_index"].apply(list)
        branch_lens = [np.sum(self.nodes["length"][np.asarray(i)]) for i in inds_branch]
        endpoints = []

        # Different levels will get a different "angle" at which the children emerge from
        # the parents. This angle is defined by the `y_offset_multiplier`. This value
        # defines the range between y-location of the first and of the last child of a
        # parent.
        y_offset_multiplier = np.linspace(
            max_y_multiplier, min_y_multiplier, np.max(levels) + 1
        )

        for b in range(self.total_nbranches):
            # For networks with mixed SWC and from-scatch neurons, only update those
            # branches that do not have coordingates yet.
            if np.any(np.isnan(self.xyzr[b])):
                if parents[b] > -1:
                    start_point = endpoints[parents[b]]
                    num_children_of_parent = num_children[parents[b]]
                    if num_children_of_parent > 1:
                        y_offset = (
                            ((index_of_child[b] / (num_children_of_parent - 1))) - 0.5
                        ) * y_offset_multiplier[levels[b]]
                    else:
                        y_offset = 0.0
                else:
                    start_point = [0, 0, 0]
                    y_offset = 0.0

                len_of_path = np.sqrt(y_offset**2 + 1.0)

                end_point = [
                    start_point[0] + branch_lens[b] / len_of_path * 1.0,
                    start_point[1] + branch_lens[b] / len_of_path * y_offset,
                    start_point[2],
                ]
                endpoints.append(end_point)

                self.xyzr[b][:, :3] = np.asarray([start_point, end_point])
            else:
                # Dummy to keey the index `endpoints[parent[b]]` above working.
                endpoints.append(np.zeros((2,)))

    def move(
        self, x: float = 0.0, y: float = 0.0, z: float = 0.0, update_nodes: bool = True
    ):
        """Move cells or networks by adding to their (x, y, z) coordinates.

        This function is used only for visualization. It does not affect the simulation.

        Args:
            x: The amount to move in the x direction in um.
            y: The amount to move in the y direction in um.
            z: The amount to move in the z direction in um.
            update_nodes: Whether `.nodes` should be updated or not. Setting this to
                `False` largely speeds up moving, especially for big networks, but
                `.nodes` or `.show` will not show the new xyz coordinates.
        """
        self._move(x, y, z, self.nodes, update_nodes)

    def _move(self, x: float, y: float, z: float, view, update_nodes: bool):
        # Need to cast to set because this will return one columnn per compartment,
        # not one column per branch.
        indizes = set(view["branch_index"].to_numpy().tolist())
        for i in indizes:
            self.xyzr[i][:, 0] += x
            self.xyzr[i][:, 1] += y
            self.xyzr[i][:, 2] += z
        if update_nodes:
            self._update_nodes_with_xyz()

    def move_to(
        self,
        x: Union[float, np.ndarray] = 0.0,
        y: Union[float, np.ndarray] = 0.0,
        z: Union[float, np.ndarray] = 0.0,
        update_nodes: bool = True,
    ):
        """Move cells or networks to a location (x, y, z).

        If x, y, and z are floats, then the first compartment of the first branch
        of the first cell is moved to that float coordinate, and everything else is
        shifted by the difference between that compartment's previous coordinate and
        the new float location.

        If x, y, and z are arrays, then they must each have a length equal to the number
        of cells being moved. Then the first compartment of the first branch of each
        cell is moved to the specified location.

        Args:
            update_nodes: Whether `.nodes` should be updated or not. Setting this to
                `False` largely speeds up moving, especially for big networks, but
                `.nodes` or `.show` will not show the new xyz coordinates.
        """
        self._move_to(x, y, z, self.nodes, update_nodes)

    def _move_to(
        self,
        x: Union[float, np.ndarray],
        y: Union[float, np.ndarray],
        z: Union[float, np.ndarray],
        view: pd.DataFrame,
        update_nodes: bool,
    ):
        # Test if any coordinate values are NaN which would greatly affect moving
        if np.any(np.concatenate(self.xyzr, axis=0)[:, :3] == np.nan):
            raise ValueError(
                "NaN coordinate values detected. Shift amounts cannot be computed. Please run compute_xyzr() or assign initial coordinate values."
            )

        # Get the indices of the cells and branches to move
        cell_inds = list(view.cell_index.unique())
        branch_inds = view.branch_index.unique()

        if (
            isinstance(x, np.ndarray)
            and isinstance(y, np.ndarray)
            and isinstance(z, np.ndarray)
        ):
            assert (
                x.shape == y.shape == z.shape == (len(cell_inds),)
            ), "x, y, and z array shapes are not all equal to the number of cells to be moved."

            # Split the branches by cell id
            tup_indices = np.array([view.cell_index, view.branch_index])
            view_cell_branch_inds = np.unique(tup_indices, axis=1)[0]
            _, branch_split_inds = np.unique(view_cell_branch_inds, return_index=True)
            branches_by_cell = np.split(
                view.branch_index.unique(), branch_split_inds[1:]
            )

            # Calculate the amount to shift all of the branches of each cell
            shift_amounts = (
                np.array([x, y, z]).T - np.stack(self[cell_inds, 0].xyzr)[:, 0, :3]
            )

        else:
            # Treat as if all branches belong to the same cell to be moved
            branches_by_cell = [branch_inds]
            # Calculate the amount to shift all branches by the 1st branch of 1st cell
            shift_amounts = [np.array([x, y, z]) - self[cell_inds].xyzr[0][0, :3]]

        # Move all of the branches
        for i, branches in enumerate(branches_by_cell):
            for b in branches:
                self.xyzr[b][:, :3] += shift_amounts[i]

        if update_nodes:
            self._update_nodes_with_xyz()

    def rotate(self, degrees: float, rotation_axis: str = "xy"):
        """Rotate jaxley modules clockwise. Used only for visualization.

        This function is used only for visualization. It does not affect the simulation.

        Args:
            degrees: How many degrees to rotate the module by.
            rotation_axis: Either of {`xy` | `xz` | `yz`}.
        """
        self._rotate(degrees=degrees, rotation_axis=rotation_axis, view=self.nodes)

    def _rotate(self, degrees: float, rotation_axis: str, view: pd.DataFrame):
        degrees = degrees / 180 * np.pi
        if rotation_axis == "xy":
            dims = [0, 1]
        elif rotation_axis == "xz":
            dims = [0, 2]
        elif rotation_axis == "yz":
            dims = [1, 2]
        else:
            raise ValueError

        rotation_matrix = np.asarray(
            [[np.cos(degrees), np.sin(degrees)], [-np.sin(degrees), np.cos(degrees)]]
        )
        indizes = set(view["branch_index"].to_numpy().tolist())
        for i in indizes:
            rot = np.dot(rotation_matrix, self.xyzr[i][:, dims].T).T
            self.xyzr[i][:, dims] = rot

    @property
    def shape(self) -> Tuple[int]:
        """Returns the number of submodules contained in a module.

        ```
        network.shape = (num_cells, num_branches, num_compartments)
        cell.shape = (num_branches, num_compartments)
        branch.shape = (num_compartments,)
        ```"""
        mod_name = self.__class__.__name__.lower()
        if "comp" in mod_name:
            return (1,)
        elif "branch" in mod_name:
            return self[:].shape[1:]
        return self[:].shape

    def __getitem__(self, index):
        return self._getitem(self, index)

    def _getitem(
        self,
        module: Union["Module", "View"],
        index: Union[Tuple, int],
        child_name: Optional[str] = None,
    ) -> "View":
        """Return View which is created from indexing the module.

        Args:
            module: The module to be indexed. Will be a `Module` if `._getitem` is
                called from `__getitem__` in a `Module` and will be a `View` if it was
                called from `__getitem__` in a `View`.
            index: The index (or indices) to index the module.
            child_name: If passed, this will be the key that is used to index the
                `module`, e.g. if it is the string `branch` then we will try to call
                `module.xyz(index)`. If `None` then we try to infer automatically what
                the childview should be, given the name of the `module`.

        Returns:
            An indexed `View`.
        """
        if isinstance(index, tuple):
            if len(index) > 1:
                return childview(module, index[0], child_name)[index[1:]]
            return childview(module, index[0], child_name)
        return childview(module, index, child_name)

    def __iter__(self):
        for i in range(self.shape[0]):
            yield self[i]

    def _local_inds_to_global(
        self, cell_inds: np.ndarray, branch_inds: np.ndarray, comp_inds: np.ndarray
    ):
        """Given local inds of cell, branch, and comp, return the global comp index."""
        global_ind = (
            self.cumsum_nbranches[cell_inds] + branch_inds
        ) * self.nseg + comp_inds
        return global_ind.astype(int)

initialized property

Whether the Module is ready to be solved or not.

shape: Tuple[int] property

Returns the number of submodules contained in a module.

network.shape = (num_cells, num_branches, num_compartments)
cell.shape = (num_branches, num_compartments)
branch.shape = (num_compartments,)

add_to_group(group_name)

Add a view of the module to a group.

Groups can then be indexed. For example:

net.cell(0).add_to_group("excitatory")
net.excitatory.set("radius", 0.1)

Parameters:

Name	Type	Description	Default
group_name	str	The name of the group.	required

Source code in jaxley/modules/base.py

def add_to_group(self, group_name: str):
    """Add a view of the module to a group.

    Groups can then be indexed. For example:
    ```python
    net.cell(0).add_to_group("excitatory")
    net.excitatory.set("radius", 0.1)
    ```

    Args:
        group_name: The name of the group.
    """
    raise ValueError("`add_to_group()` makes no sense for an entire module.")

clamp(state_name, state_array, verbose=True)

Clamp a state to a given value across specified compartments.

Parameters:

Name	Type	Description	Default
state_name	str	The name of the state to clamp.	required
state_array	nd	Array of values to clamp the state to.	required
verbose		If True, prints details about the clamping.	True

This function sets external states for the compartments.

Source code in jaxley/modules/base.py

def clamp(self, state_name: str, state_array: jnp.ndarray, verbose: bool = True):
    """Clamp a state to a given value across specified compartments.

    Args:
        state_name: The name of the state to clamp.
        state_array (jnp.nd: Array of values to clamp the state to.
        verbose : If True, prints details about the clamping.

    This function sets external states for the compartments.
    """
    if state_name not in self.nodes.columns:
        raise KeyError(f"{state_name} is not a recognized state in this module.")
    self._external_input(state_name, state_array, self.nodes, verbose=verbose)

compute_xyz()

Return xyz coordinates of every branch, based on the branch length.

This function should not be called if the morphology was read from an .swc file. However, for morphologies that were constructed from scratch, this function must be called before .vis(). The computed xyz coordinates are only used for plotting.

Source code in jaxley/modules/base.py

def compute_xyz(self):
    """Return xyz coordinates of every branch, based on the branch length.

    This function should not be called if the morphology was read from an `.swc`
    file. However, for morphologies that were constructed from scratch, this
    function **must** be called before `.vis()`. The computed `xyz` coordinates
    are only used for plotting.
    """
    max_y_multiplier = 5.0
    min_y_multiplier = 0.5

    parents = self.comb_parents
    num_children = _compute_num_children(parents)
    index_of_child = _compute_index_of_child(parents)
    levels = compute_levels(parents)

    # Extract branch.
    inds_branch = self.nodes.groupby("branch_index")["comp_index"].apply(list)
    branch_lens = [np.sum(self.nodes["length"][np.asarray(i)]) for i in inds_branch]
    endpoints = []

    # Different levels will get a different "angle" at which the children emerge from
    # the parents. This angle is defined by the `y_offset_multiplier`. This value
    # defines the range between y-location of the first and of the last child of a
    # parent.
    y_offset_multiplier = np.linspace(
        max_y_multiplier, min_y_multiplier, np.max(levels) + 1
    )

    for b in range(self.total_nbranches):
        # For networks with mixed SWC and from-scatch neurons, only update those
        # branches that do not have coordingates yet.
        if np.any(np.isnan(self.xyzr[b])):
            if parents[b] > -1:
                start_point = endpoints[parents[b]]
                num_children_of_parent = num_children[parents[b]]
                if num_children_of_parent > 1:
                    y_offset = (
                        ((index_of_child[b] / (num_children_of_parent - 1))) - 0.5
                    ) * y_offset_multiplier[levels[b]]
                else:
                    y_offset = 0.0
            else:
                start_point = [0, 0, 0]
                y_offset = 0.0

            len_of_path = np.sqrt(y_offset**2 + 1.0)

            end_point = [
                start_point[0] + branch_lens[b] / len_of_path * 1.0,
                start_point[1] + branch_lens[b] / len_of_path * y_offset,
                start_point[2],
            ]
            endpoints.append(end_point)

            self.xyzr[b][:, :3] = np.asarray([start_point, end_point])
        else:
            # Dummy to keey the index `endpoints[parent[b]]` above working.
            endpoints.append(np.zeros((2,)))

data_set(key, val, param_state)

Set parameter of module (or its view) to a new value within jit.

Parameters:

Name	Type	Description	Default
key	str	The name of the parameter to set.	required
val	Union[float, ndarray]	The value to set the parameter to. If it is jnp.ndarray then it must be of shape (len(num_compartments)).	required
param_state	Optional[List[Dict]]	State of the setted parameters, internally used such that this function does not modify global state.	required

Source code in jaxley/modules/base.py

def data_set(
    self,
    key: str,
    val: Union[float, jnp.ndarray],
    param_state: Optional[List[Dict]],
):
    """Set parameter of module (or its view) to a new value within `jit`.

    Args:
        key: The name of the parameter to set.
        val: The value to set the parameter to. If it is `jnp.ndarray` then it
            must be of shape `(len(num_compartments))`.
        param_state: State of the setted parameters, internally used such that this
            function does not modify global state.
    """
    view = (
        self.edges
        if key in self.synapse_param_names or key in self.synapse_state_names
        else self.nodes
    )
    return self._data_set(key, val, view, param_state=param_state)

data_stimulate(current, data_stimuli=None, verbose=False)

Insert a stimulus into the module within jit (or grad).

Parameters:

Name	Type	Description	Default
current	ndarray	Current in nA.	required
verbose	bool	Whether or not to print the number of inserted stimuli. False by default because this method is meant to be jitted.	False

Source code in jaxley/modules/base.py

def data_stimulate(
    self,
    current: jnp.ndarray,
    data_stimuli: Optional[Tuple[jnp.ndarray, pd.DataFrame]] = None,
    verbose: bool = False,
) -> Tuple[jnp.ndarray, pd.DataFrame]:
    """Insert a stimulus into the module within jit (or grad).

    Args:
        current: Current in `nA`.
        verbose: Whether or not to print the number of inserted stimuli. `False`
            by default because this method is meant to be jitted.
    """
    return self._data_stimulate(current, data_stimuli, self.nodes, verbose=verbose)

delete_recordings()

Removes all recordings from the module.

Source code in jaxley/modules/base.py

def delete_recordings(self):
    """Removes all recordings from the module."""
    self.recordings = pd.DataFrame().from_dict({})

delete_stimuli()

Removes all stimuli from the module.

Source code in jaxley/modules/base.py

def delete_stimuli(self):
    """Removes all stimuli from the module."""
    self.externals.pop("i", None)
    self.external_inds.pop("i", None)

delete_trainables()

Removes all trainable parameters from the module.

Source code in jaxley/modules/base.py

def delete_trainables(self):
    """Removes all trainable parameters from the module."""
    self.indices_set_by_trainables: List[jnp.ndarray] = []
    self.trainable_params: List[Dict[str, jnp.ndarray]] = []
    self.num_trainable_params: int = 0

get_all_parameters(pstate)

Return all parameters (and coupling conductances) needed to simulate.

Runs init_conds() and return every parameter that is needed to solve the ODE. This includes conductances, radiuses, lengths, axial_resistivities, but also coupling conductances.

This is done by first obtaining the current value of every parameter (not only the trainable ones) and then replacing the trainable ones with the value in trainable_params(). This function is run within jx.integrate().

pstate can be obtained by calling params_to_pstate().

params = module.get_parameters() # i.e. [0, 1, 2]
pstate = params_to_pstate(params, module.indices_set_by_trainables)
module.to_jax() # needed for call to module.jaxnodes

Parameters:

Name	Type	Description	Default
pstate	List[Dict]	The state of the trainable parameters. pstate takes the form [{“key”: “gNa”, “indices”: jnp.array([0, 1, 2]), “val”: jnp.array([0.1, 0.2, 0.3])}, …].	required

Returns:

Type	Description
Dict[str, ndarray]	A dictionary of all module parameters.

Source code in jaxley/modules/base.py

def get_all_parameters(self, pstate: List[Dict]) -> Dict[str, jnp.ndarray]:
    """Return all parameters (and coupling conductances) needed to simulate.

    Runs `init_conds()` and return every parameter that is needed to solve the ODE.
    This includes conductances, radiuses, lengths, axial_resistivities, but also
    coupling conductances.

    This is done by first obtaining the current value of every parameter (not only
    the trainable ones) and then replacing the trainable ones with the value
    in `trainable_params()`. This function is run within `jx.integrate()`.

    pstate can be obtained by calling `params_to_pstate()`.
    ```
    params = module.get_parameters() # i.e. [0, 1, 2]
    pstate = params_to_pstate(params, module.indices_set_by_trainables)
    module.to_jax() # needed for call to module.jaxnodes
    ```

    Args:
        pstate: The state of the trainable parameters. pstate takes the form
            [{"key": "gNa", "indices": jnp.array([0, 1, 2]), "val": jnp.array([0.1, 0.2, 0.3])}, ...].

    Returns:
        A dictionary of all module parameters.
    """
    params = {}
    for key in ["radius", "length", "axial_resistivity", "capacitance"]:
        params[key] = self.jaxnodes[key]

    for channel in self.channels:
        for channel_params in channel.channel_params:
            params[channel_params] = self.jaxnodes[channel_params]

    for synapse_params in self.synapse_param_names:
        params[synapse_params] = self.jaxedges[synapse_params]

    # Override with those parameters set by `.make_trainable()`.
    for parameter in pstate:
        key = parameter["key"]
        inds = parameter["indices"]
        set_param = parameter["val"]
        if key in params:  # Only parameters, not initial states.
            # `inds` is of shape `(num_params, num_comps_per_param)`.
            # `set_param` is of shape `(num_params,)`
            # We need to unsqueeze `set_param` to make it `(num_params, 1)` for the
            # `.set()` to work. This is done with `[:, None]`.
            params[key] = params[key].at[inds].set(set_param[:, None])

    # Compute conductance params and append them.
    cond_params = self.init_conds(params)
    for key in cond_params:
        params[key] = cond_params[key]

    return params

get_all_states(pstate, all_params, delta_t)

Get the full initial state of the module from jaxnodes and trainables.

Parameters:

Name	Type	Description	Default
pstate	List[Dict]	The state of the trainable parameters.	required
all_params		All parameters of the module.	required
delta_t	float	The time step.	required

Returns:

Type	Description
Dict[str, ndarray]	A dictionary of all states of the module.

Source code in jaxley/modules/base.py

def get_all_states(
    self, pstate: List[Dict], all_params, delta_t: float
) -> Dict[str, jnp.ndarray]:
    """Get the full initial state of the module from jaxnodes and trainables.

    Args:
        pstate: The state of the trainable parameters.
        all_params: All parameters of the module.
        delta_t: The time step.

    Returns:
        A dictionary of all states of the module.
    """
    states = self.get_states_from_nodes_and_edges()

    # Override with the initial states set by `.make_trainable()`.
    for parameter in pstate:
        key = parameter["key"]
        inds = parameter["indices"]
        set_param = parameter["val"]
        if key in states:  # Only initial states, not parameters.
            # `inds` is of shape `(num_params, num_comps_per_param)`.
            # `set_param` is of shape `(num_params,)`
            # We need to unsqueeze `set_param` to make it `(num_params, 1)` for the
            # `.set()` to work. This is done with `[:, None]`.
            states[key] = states[key].at[inds].set(set_param[:, None])

    # Add to the states the initial current through every channel.
    states, _ = self._channel_currents(
        states, delta_t, self.channels, self.nodes, all_params
    )

    # Add to the states the initial current through every synapse.
    states, _ = self._synapse_currents(
        states, self.synapses, all_params, delta_t, self.edges
    )
    return states

get_parameters()

Get all trainable parameters.

The returned parameters should be passed to `jx.integrate(…, params=params).

Returns:

Type	Description
List[Dict[str, ndarray]]	A list of all trainable parameters in the form of [{“gNa”: jnp.array([0.1, 0.2, 0.3])}, …].

Source code in jaxley/modules/base.py

def get_parameters(self) -> List[Dict[str, jnp.ndarray]]:
    """Get all trainable parameters.

    The returned parameters should be passed to `jx.integrate(..., params=params).

    Returns:
        A list of all trainable parameters in the form of
            [{"gNa": jnp.array([0.1, 0.2, 0.3])}, ...].
    """
    return self.trainable_params

get_states_from_nodes_and_edges()

Return states as they are set in the .nodes and .edges tables.

Source code in jaxley/modules/base.py

def get_states_from_nodes_and_edges(self):
    """Return states as they are set in the `.nodes` and `.edges` tables."""
    self.to_jax()  # Create `.jaxnodes` from `.nodes` and `.jaxedges` from `.edges`.
    states = {"v": self.jaxnodes["v"]}
    # Join node and edge states into a single state dictionary.
    for channel in self.channels:
        for channel_states in channel.channel_states:
            states[channel_states] = self.jaxnodes[channel_states]
    for synapse_states in self.synapse_state_names:
        states[synapse_states] = self.jaxedges[synapse_states]
    return states

init_conds(params) abstractmethod

Initialize coupling conductances.

Parameters:

Name	Type	Description	Default
params	Dict	Conductances and morphology parameters, not yet including coupling conductances.	required

Source code in jaxley/modules/base.py

@abstractmethod
def init_conds(self, params: Dict):
    """Initialize coupling conductances.

    Args:
        params: Conductances and morphology parameters, not yet including
            coupling conductances.
    """
    raise NotImplementedError

init_states(delta_t=0.025)

Initialize all mechanisms in their steady state.

This considers the voltages and parameters of each compartment.

Parameters:

Name	Type	Description	Default
delta_t	float	Passed on to channel.init_state().	0.025

Source code in jaxley/modules/base.py

def init_states(self, delta_t: float = 0.025):
    """Initialize all mechanisms in their steady state.

    This considers the voltages and parameters of each compartment.

    Args:
        delta_t: Passed on to `channel.init_state()`.
    """
    # Update states of the channels.
    channel_nodes = self.nodes
    states = self.get_states_from_nodes_and_edges()

    # We do not use any `pstate` for initializing. In principle, we could change
    # that by allowing an input `params` and `pstate` to this function.
    params = self.get_all_parameters([])

    for channel in self.channels:
        name = channel._name
        channel_indices = channel_nodes.loc[channel_nodes[name]][
            "comp_index"
        ].to_numpy()
        voltages = channel_nodes.loc[channel_indices, "v"].to_numpy()

        channel_param_names = list(channel.channel_params.keys())
        channel_state_names = list(channel.channel_states.keys())
        channel_states = query_channel_states_and_params(
            states, channel_state_names, channel_indices
        )
        channel_params = query_channel_states_and_params(
            params, channel_param_names, channel_indices
        )

        init_state = channel.init_state(
            channel_states, voltages, channel_params, delta_t
        )

        # `init_state` might not return all channel states. Only the ones that are
        # returned are updated here.
        for key, val in init_state.items():
            # Note that we are overriding `self.nodes` here, but `self.nodes` is
            # not used above to actually compute the current states (so there are
            # no issues with overriding states).
            self.nodes.loc[channel_indices, key] = val

initialize()

Initialize the module.

Source code in jaxley/modules/base.py

def initialize(self):
    """Initialize the module."""
    self.init_morph()
    return self

insert(channel)

Insert a channel into the module.

Parameters:

Name	Type	Description	Default
channel	Channel	The channel to insert.	required

Source code in jaxley/modules/base.py

def insert(self, channel: Channel):
    """Insert a channel into the module.

    Args:
        channel: The channel to insert."""
    self._insert(channel, self.nodes)

make_trainable(key, init_val=None, verbose=True)

Make a parameter trainable.

If a parameter is made trainable, it will be returned by get_parameters() and should then be passed to jx.integrate(..., params=params).

Parameters:

Name	Type	Description	Default
key	str	Name of the parameter to make trainable.	required
init_val	Optional[Union[float, list]]	Initial value of the parameter. If float, the same value is used for every created parameter. If list, the length of the list has to match the number of created parameters. If None, the current parameter value is used and if parameter sharing is performed that the current parameter value is averaged over all shared parameters.	None
verbose	bool	Whether to print the number of parameters that are added and the total number of parameters.	True

Source code in jaxley/modules/base.py

def make_trainable(
    self,
    key: str,
    init_val: Optional[Union[float, list]] = None,
    verbose: bool = True,
):
    """Make a parameter trainable.

    If a parameter is made trainable, it will be returned by `get_parameters()`
    and should then be passed to `jx.integrate(..., params=params)`.

    Args:
        key: Name of the parameter to make trainable.
        init_val: Initial value of the parameter. If `float`, the same value is
            used for every created parameter. If `list`, the length of the list has
            to match the number of created parameters. If `None`, the current
            parameter value is used and if parameter sharing is performed that the
            current parameter value is averaged over all shared parameters.
        verbose: Whether to print the number of parameters that are added and the
            total number of parameters.
    """
    assert (
        key not in self.synapse_param_names and key not in self.synapse_state_names
    ), "Parameters of synapses can only be made trainable via the `SynapseView`."
    view = self.nodes
    view = deepcopy(view.assign(controlled_by_param=0))
    self._make_trainable(view, key, init_val, verbose=verbose)

move(x=0.0, y=0.0, z=0.0, update_nodes=True)

Move cells or networks by adding to their (x, y, z) coordinates.

This function is used only for visualization. It does not affect the simulation.

Parameters:

Name	Type	Description	Default
x	float	The amount to move in the x direction in um.	0.0
y	float	The amount to move in the y direction in um.	0.0
z	float	The amount to move in the z direction in um.	0.0
update_nodes	bool	Whether .nodes should be updated or not. Setting this to False largely speeds up moving, especially for big networks, but .nodes or .show will not show the new xyz coordinates.	True

Source code in jaxley/modules/base.py

def move(
    self, x: float = 0.0, y: float = 0.0, z: float = 0.0, update_nodes: bool = True
):
    """Move cells or networks by adding to their (x, y, z) coordinates.

    This function is used only for visualization. It does not affect the simulation.

    Args:
        x: The amount to move in the x direction in um.
        y: The amount to move in the y direction in um.
        z: The amount to move in the z direction in um.
        update_nodes: Whether `.nodes` should be updated or not. Setting this to
            `False` largely speeds up moving, especially for big networks, but
            `.nodes` or `.show` will not show the new xyz coordinates.
    """
    self._move(x, y, z, self.nodes, update_nodes)

move_to(x=0.0, y=0.0, z=0.0, update_nodes=True)

Move cells or networks to a location (x, y, z).

If x, y, and z are floats, then the first compartment of the first branch of the first cell is moved to that float coordinate, and everything else is shifted by the difference between that compartment’s previous coordinate and the new float location.

If x, y, and z are arrays, then they must each have a length equal to the number of cells being moved. Then the first compartment of the first branch of each cell is moved to the specified location.

Parameters:

Name	Type	Description	Default
update_nodes	bool	Whether .nodes should be updated or not. Setting this to False largely speeds up moving, especially for big networks, but .nodes or .show will not show the new xyz coordinates.	True

Source code in jaxley/modules/base.py

def move_to(
    self,
    x: Union[float, np.ndarray] = 0.0,
    y: Union[float, np.ndarray] = 0.0,
    z: Union[float, np.ndarray] = 0.0,
    update_nodes: bool = True,
):
    """Move cells or networks to a location (x, y, z).

    If x, y, and z are floats, then the first compartment of the first branch
    of the first cell is moved to that float coordinate, and everything else is
    shifted by the difference between that compartment's previous coordinate and
    the new float location.

    If x, y, and z are arrays, then they must each have a length equal to the number
    of cells being moved. Then the first compartment of the first branch of each
    cell is moved to the specified location.

    Args:
        update_nodes: Whether `.nodes` should be updated or not. Setting this to
            `False` largely speeds up moving, especially for big networks, but
            `.nodes` or `.show` will not show the new xyz coordinates.
    """
    self._move_to(x, y, z, self.nodes, update_nodes)

record(state='v', verbose=True)

Insert a recording into the compartment.

Parameters:

Name	Type	Description	Default
state	str	The name of the state to record.	'v'
verbose	bool	Whether to print number of inserted recordings.	True

Source code in jaxley/modules/base.py

def record(self, state: str = "v", verbose: bool = True):
    """Insert a recording into the compartment.

    Args:
        state: The name of the state to record.
        verbose: Whether to print number of inserted recordings."""
    view = deepcopy(self.nodes)
    view["state"] = state
    recording_view = view[["comp_index", "state"]]
    recording_view = recording_view.rename(columns={"comp_index": "rec_index"})
    self._record(recording_view, verbose=verbose)

rotate(degrees, rotation_axis='xy')

Rotate jaxley modules clockwise. Used only for visualization.

This function is used only for visualization. It does not affect the simulation.

Parameters:

Name	Type	Description	Default
degrees	float	How many degrees to rotate the module by.	required
rotation_axis	str	Either of {xy | xz | yz}.	'xy'

Source code in jaxley/modules/base.py

def rotate(self, degrees: float, rotation_axis: str = "xy"):
    """Rotate jaxley modules clockwise. Used only for visualization.

    This function is used only for visualization. It does not affect the simulation.

    Args:
        degrees: How many degrees to rotate the module by.
        rotation_axis: Either of {`xy` | `xz` | `yz`}.
    """
    self._rotate(degrees=degrees, rotation_axis=rotation_axis, view=self.nodes)

set(key, val)

Set parameter of module (or its view) to a new value.

Note that this function can not be called within jax.jit or jax.grad. Instead, it should be used set the parameters of the module before the simulation. Use .data_set() to set parameters during jax.jit or jax.grad.

Parameters:

Name	Type	Description	Default
key	str	The name of the parameter to set.	required
val	Union[float, ndarray]	The value to set the parameter to. If it is jnp.ndarray then it must be of shape (len(num_compartments)).	required

Source code in jaxley/modules/base.py

def set(self, key: str, val: Union[float, jnp.ndarray]):
    """Set parameter of module (or its view) to a new value.

    Note that this function can not be called within `jax.jit` or `jax.grad`.
    Instead, it should be used set the parameters of the module **before** the
    simulation. Use `.data_set()` to set parameters during `jax.jit` or
    `jax.grad`.

    Args:
        key: The name of the parameter to set.
        val: The value to set the parameter to. If it is `jnp.ndarray` then it
            must be of shape `(len(num_compartments))`.
    """
    # TODO(@michaeldeistler) should we allow `.set()` for synaptic parameters
    # without using the `SynapseView`, purely for consistency with `make_trainable`?
    view = (
        self.edges
        if key in self.synapse_param_names or key in self.synapse_state_names
        else self.nodes
    )
    self._set(key, val, view, view)

show(param_names=None, *, indices=True, params=True, states=True, channel_names=None)

Print detailed information about the Module or a view of it.

Parameters:

Name	Type	Description	Default
param_names	Optional[Union[str, List[str]]]	The names of the parameters to show. If None, all parameters are shown. NOT YET IMPLEMENTED.	None
indices	bool	Whether to show the indices of the compartments.	True
params	bool	Whether to show the parameters of the compartments.	True
states	bool	Whether to show the states of the compartments.	True
channel_names	Optional[List[str]]	The names of the channels to show. If None, all channels are shown.	None

Returns:

Type	Description
DataFrame	A pd.DataFrame with the requested information.

Source code in jaxley/modules/base.py

def show(
    self,
    param_names: Optional[Union[str, List[str]]] = None,  # TODO.
    *,
    indices: bool = True,
    params: bool = True,
    states: bool = True,
    channel_names: Optional[List[str]] = None,
) -> pd.DataFrame:
    """Print detailed information about the Module or a view of it.

    Args:
        param_names: The names of the parameters to show. If `None`, all parameters
            are shown. NOT YET IMPLEMENTED.
        indices: Whether to show the indices of the compartments.
        params: Whether to show the parameters of the compartments.
        states: Whether to show the states of the compartments.
        channel_names: The names of the channels to show. If `None`, all channels are
            shown.

    Returns:
        A `pd.DataFrame` with the requested information.
    """
    return self._show(
        self.nodes, param_names, indices, params, states, channel_names
    )

step(u, delta_t, external_inds, externals, params, solver='bwd_euler', voltage_solver='jaxley.stone')

One step of solving the Ordinary Differential Equation.

This function is called inside of integrate and increments the state of the module by one time step. Calls _step_channels and _step_synapse to update the states of the channels and synapses using fwd_euler.

Parameters:

Name	Type	Description	Default
u	Dict[str, ndarray]	The state of the module. voltages = u[“v”]	required
delta_t	float	The time step.	required
external_inds	Dict[str, ndarray]	The indices of the external inputs.	required
externals	Dict[str, ndarray]	The external inputs.	required
params	Dict[str, ndarray]	The parameters of the module.	required
solver	str	The solver to use for the voltages. Either of [“bwd_euler”, “fwd_euler”, “crank_nicolson”].	'bwd_euler'
voltage_solver	str	The tridiagonal solver used to diagonalize the coefficient matrix of the ODE system. Either of [“jaxley.thomas”, “jaxley.stone”].	'jaxley.stone'

Returns:

Type	Description
Dict[str, ndarray]	The updated state of the module.

Source code in jaxley/modules/base.py

def step(
    self,
    u: Dict[str, jnp.ndarray],
    delta_t: float,
    external_inds: Dict[str, jnp.ndarray],
    externals: Dict[str, jnp.ndarray],
    params: Dict[str, jnp.ndarray],
    solver: str = "bwd_euler",
    voltage_solver: str = "jaxley.stone",
) -> Dict[str, jnp.ndarray]:
    """One step of solving the Ordinary Differential Equation.

    This function is called inside of `integrate` and increments the state of the
    module by one time step. Calls `_step_channels` and `_step_synapse` to update
    the states of the channels and synapses using fwd_euler.

    Args:
        u: The state of the module. voltages = u["v"]
        delta_t: The time step.
        external_inds: The indices of the external inputs.
        externals: The external inputs.
        params: The parameters of the module.
        solver: The solver to use for the voltages. Either of ["bwd_euler",
            "fwd_euler", "crank_nicolson"].
        voltage_solver: The tridiagonal solver used to diagonalize the
            coefficient matrix of the ODE system. Either of ["jaxley.thomas",
            "jaxley.stone"].

    Returns:
        The updated state of the module.
    """

    # Extract the voltages
    voltages = u["v"]

    # Extract the external inputs
    has_current = "i" in externals.keys()
    i_current = externals["i"] if has_current else jnp.asarray([]).astype("float")
    i_inds = external_inds["i"] if has_current else jnp.asarray([]).astype("int32")
    i_ext = self._get_external_input(
        voltages, i_inds, i_current, params["radius"], params["length"]
    )

    # Step of the channels.
    u, (v_terms, const_terms) = self._step_channels(
        u, delta_t, self.channels, self.nodes, params
    )

    # Step of the synapse.
    u, (syn_v_terms, syn_const_terms) = self._step_synapse(
        u,
        self.synapses,
        params,
        delta_t,
        self.edges,
    )

    # Clamp for channels and synapses.
    for key in externals.keys():
        if key not in ["i", "v"]:
            u[key] = u[key].at[external_inds[key]].set(externals[key])

    # Voltage steps.
    cm = params["capacitance"]  # Abbreviation.

    solver_kwargs = {
        "voltages": voltages,
        "voltage_terms": (v_terms + syn_v_terms) / cm,
        "constant_terms": (const_terms + i_ext + syn_const_terms) / cm,
        "coupling_conds_upper": params["branch_uppers"],
        "coupling_conds_lower": params["branch_lowers"],
        "summed_coupling_conds": params["branch_diags"],
        "branchpoint_conds_children": params["branchpoint_conds_children"],
        "branchpoint_conds_parents": params["branchpoint_conds_parents"],
        "branchpoint_weights_children": params["branchpoint_weights_children"],
        "branchpoint_weights_parents": params["branchpoint_weights_parents"],
        "par_inds": self.par_inds,
        "child_inds": self.child_inds,
        "nbranches": self.total_nbranches,
        "solver": voltage_solver,
        "children_in_level": self.children_in_level,
        "parents_in_level": self.parents_in_level,
        "root_inds": self.root_inds,
        "branchpoint_group_inds": self.branchpoint_group_inds,
        "debug_states": self.debug_states,
    }
    if solver == "bwd_euler":
        new_voltages = step_voltage_implicit(**solver_kwargs, delta_t=delta_t)
        u["v"] = new_voltages.ravel(order="C")
    elif solver == "fwd_euler":
        new_voltages = step_voltage_explicit(**solver_kwargs, delta_t=delta_t)
        u["v"] = new_voltages.ravel(order="C")
    elif solver == "crank_nicolson":
        # Crank Nicolson advances by half a step of backward and half a step of
        # forward Euler.
        half_step_delta_t = delta_t / 2
        half_step_voltages = step_voltage_implicit(
            **solver_kwargs, delta_t=half_step_delta_t
        )
        # The forward Euler step in Crank Nicolson can be performed easily as
        # `V_{n+1} = 2 * V_{n+1/2} - V_n`. See also NEURON book Chapter 4.
        u["v"] = 2 * half_step_voltages.ravel(order="C") - voltages
    else:
        raise ValueError(
            f"You specified `solver={solver}`. The only allowed solvers are "
            "['bwd_euler', 'fwd_euler', 'crank_nicolson']."
        )

    # Clamp for voltages.
    if "v" in externals.keys():
        u["v"] = u["v"].at[external_inds["v"]].set(externals["v"])

    return u

stimulate(current=None, verbose=True)

Insert a stimulus into the compartment.

current must be a 1d array or have batch dimension of size (num_compartments, ) or (1, ). If 1d, the same stimulus is added to all compartments.

This function cannot be run during jax.jit and jax.grad. Because of this, it should only be used for static stimuli (i.e., stimuli that do not depend on the data and that should not be learned). For stimuli that depend on data (or that should be learned), please use data_stimulate().

Parameters:

Name	Type	Description	Default
current	Optional[ndarray]	Current in nA.	None

Source code in jaxley/modules/base.py

def stimulate(self, current: Optional[jnp.ndarray] = None, verbose: bool = True):
    """Insert a stimulus into the compartment.

    current must be a 1d array or have batch dimension of size `(num_compartments, )`
    or `(1, )`. If 1d, the same stimulus is added to all compartments.

    This function cannot be run during `jax.jit` and `jax.grad`. Because of this,
    it should only be used for static stimuli (i.e., stimuli that do not depend
    on the data and that should not be learned). For stimuli that depend on data
    (or that should be learned), please use `data_stimulate()`.

    Args:
        current: Current in `nA`.
    """
    self._external_input("i", current, self.nodes, verbose=verbose)

to_jax()

Move .nodes to .jaxnodes.

Before the actual simulation is run (via jx.integrate), all parameters of the jx.Module are stored in .nodes (a pd.DataFrame). However, for simulation, these parameters have to be moved to be jnp.ndarrays such that they can be processed on GPU/TPU and such that the simulation can be differentiated. .to_jax() copies the .nodes to .jaxnodes.

Source code in jaxley/modules/base.py

def to_jax(self):
    """Move `.nodes` to `.jaxnodes`.

    Before the actual simulation is run (via `jx.integrate`), all parameters of
    the `jx.Module` are stored in `.nodes` (a `pd.DataFrame`). However, for
    simulation, these parameters have to be moved to be `jnp.ndarrays` such that
    they can be processed on GPU/TPU and such that the simulation can be
    differentiated. `.to_jax()` copies the `.nodes` to `.jaxnodes`.
    """
    self.jaxnodes = {}
    for key, value in self.nodes.to_dict(orient="list").items():
        inds = jnp.arange(len(value))
        self.jaxnodes[key] = jnp.asarray(value)[inds]

    # `jaxedges` contains only parameters (no indices).
    # `jaxedges` contains only non-Nan elements. This is unlike the channels where
    # we allow parameter sharing.
    self.jaxedges = {}
    edges = self.edges.to_dict(orient="list")
    for i, synapse in enumerate(self.synapses):
        for key in synapse.synapse_params:
            condition = np.asarray(edges["type_ind"]) == i
            self.jaxedges[key] = jnp.asarray(np.asarray(edges[key])[condition])
        for key in synapse.synapse_states:
            self.jaxedges[key] = jnp.asarray(np.asarray(edges[key])[condition])

vis(ax=None, col='k', dims=(0, 1), type='line', morph_plot_kwargs={})

Visualize the module.

Parameters:

Name	Type	Description	Default
ax	Optional[Axes]	An axis into which to plot.	None
col	str	The color for all branches.	'k'
dims	Tuple[int]	Which dimensions to plot. 1=x, 2=y, 3=z coordinate. Must be a tuple of two of them.	(0, 1)
morph_plot_kwargs	Dict	Keyword arguments passed to the plotting function.	{}

Source code in jaxley/modules/base.py

def vis(
    self,
    ax: Optional[Axes] = None,
    col: str = "k",
    dims: Tuple[int] = (0, 1),
    type: str = "line",
    morph_plot_kwargs: Dict = {},
) -> Axes:
    """Visualize the module.

    Args:
        ax: An axis into which to plot.
        col: The color for all branches.
        dims: Which dimensions to plot. 1=x, 2=y, 3=z coordinate. Must be a tuple of
            two of them.
        morph_plot_kwargs: Keyword arguments passed to the plotting function.
    """
    return self._vis(
        dims=dims,
        col=col,
        ax=ax,
        view=self.nodes,
        type=type,
        morph_plot_kwargs=morph_plot_kwargs,
    )

Compartment

Bases: Module

Compartment class.

This class defines a single compartment that can be simulated by itself or connected up into branches. It is the basic building block of a neuron model.

Source code in jaxley/modules/compartment.py

class Compartment(Module):
    """Compartment class.

    This class defines a single compartment that can be simulated by itself or
    connected up into branches. It is the basic building block of a neuron model.
    """

    compartment_params: Dict = {
        "length": 10.0,  # um
        "radius": 1.0,  # um
        "axial_resistivity": 5_000.0,  # ohm cm
        "capacitance": 1.0,  # uF/cm^2
    }
    compartment_states: Dict = {"v": -70.0}

    def __init__(self):
        super().__init__()

        self.nseg = 1
        self.total_nbranches = 1
        self.nbranches_per_cell = [1]
        self.cumsum_nbranches = jnp.asarray([0, 1])

        # Setting up the `nodes` for indexing.
        self.nodes = pd.DataFrame(
            dict(comp_index=[0], branch_index=[0], cell_index=[0])
        )
        self._append_params_and_states(self.compartment_params, self.compartment_states)

        # Synapses.
        self.branch_edges = pd.DataFrame(
            dict(parent_branch_index=[], child_branch_index=[])
        )

        # For morphology indexing.
        self.child_inds = np.asarray([]).astype(int)
        self.child_belongs_to_branchpoint = np.asarray([]).astype(int)
        self.par_inds = np.asarray([]).astype(int)
        self.total_nbranchpoints = 0
        self.branchpoint_group_inds = np.asarray([]).astype(int)

        self.children_in_level = []
        self.parents_in_level = []
        self.root_inds = jnp.asarray([0])

        # Initialize the module.
        self.initialize()
        self.init_syns()
        self.initialized_conds = True

        # Coordinates.
        self.xyzr = [float("NaN") * np.zeros((2, 4))]

    def init_conds(self, params):
        return {
            "branchpoint_conds_children": jnp.asarray([]),
            "branchpoint_conds_parents": jnp.asarray([]),
            "branchpoint_weights_children": jnp.asarray([]),
            "branchpoint_weights_parents": jnp.asarray([]),
            "branch_uppers": jnp.asarray([]),
            "branch_lowers": jnp.asarray([]),
            "branch_diags": jnp.asarray([0.0]),
        }

Branch

Bases: Module

Branch class.

This class defines a single branch that can be simulated by itself or connected to build a cell. A branch is linear segment of several compartments and can be connected to no, one or more other branches at each end to build more intricate cell morphologies.

Source code in jaxley/modules/branch.py

class Branch(Module):
    """Branch class.

    This class defines a single branch that can be simulated by itself or
    connected to build a cell. A branch is linear segment of several compartments
    and can be connected to no, one or more other branches at each end to build more
    intricate cell morphologies.
    """

    branch_params: Dict = {}
    branch_states: Dict = {}

    def __init__(
        self,
        compartments: Optional[Union[Compartment, List[Compartment]]] = None,
        nseg: Optional[int] = None,
    ):
        """
        Args:
            compartments: A single compartment or a list of compartments that make up the
                branch.
            nseg: Number of segments to divide the branch into. If `compartments` is an
                a single compartment, than the compartment is repeated `nseg` times to
                create the branch.
        """
        super().__init__()
        assert (
            isinstance(compartments, (Compartment, List)) or compartments is None
        ), "Only Compartment or List[Compartment] is allowed."
        if isinstance(compartments, Compartment):
            assert (
                nseg is not None
            ), "If `compartments` is not a list then you have to set `nseg`."
        compartments = Compartment() if compartments is None else compartments
        nseg = 1 if nseg is None else nseg

        if isinstance(compartments, Compartment):
            compartment_list = [compartments] * nseg
        else:
            compartment_list = compartments

        self.nseg = len(compartment_list)
        self.total_nbranches = 1
        self.nbranches_per_cell = [1]
        self.cumsum_nbranches = jnp.asarray([0, 1])

        # Indexing.
        self.nodes = pd.concat([c.nodes for c in compartment_list], ignore_index=True)
        self._append_params_and_states(self.branch_params, self.branch_states)
        self.nodes["comp_index"] = np.arange(self.nseg).tolist()
        self.nodes["branch_index"] = [0] * self.nseg
        self.nodes["cell_index"] = [0] * self.nseg

        # Channels.
        self._gather_channels_from_constituents(compartment_list)

        # Synapse indexing.
        self.syn_edges = pd.DataFrame(
            dict(global_pre_comp_index=[], global_post_comp_index=[], type="")
        )
        self.branch_edges = pd.DataFrame(
            dict(parent_branch_index=[], child_branch_index=[])
        )

        # For morphology indexing.
        self.child_inds = np.asarray([]).astype(int)
        self.child_belongs_to_branchpoint = np.asarray([]).astype(int)
        self.par_inds = np.asarray([]).astype(int)
        self.total_nbranchpoints = 0
        self.branchpoint_group_inds = np.asarray([]).astype(int)

        self.children_in_level = []
        self.parents_in_level = []
        self.root_inds = jnp.asarray([0])

        self.initialize()
        self.init_syns()
        self.initialized_conds = False

        # Coordinates.
        self.xyzr = [float("NaN") * np.zeros((2, 4))]

    def __getattr__(self, key: str):
        # Ensure that hidden methods such as `__deepcopy__` still work.
        if key.startswith("__"):
            return super().__getattribute__(key)

        if key in ["comp", "loc"]:
            view = deepcopy(self.nodes)
            view["global_comp_index"] = view["comp_index"]
            view["global_branch_index"] = view["branch_index"]
            view["global_cell_index"] = view["cell_index"]
            compview = CompartmentView(self, view)
            return compview if key == "comp" else compview.loc
        elif key in self.group_nodes:
            inds = self.group_nodes[key].index.values
            view = self.nodes.loc[inds]
            view["global_comp_index"] = view["comp_index"]
            view["global_branch_index"] = view["branch_index"]
            view["global_cell_index"] = view["cell_index"]
            return GroupView(self, view, CompartmentView, ["comp", "loc"])
        else:
            raise KeyError(f"Key {key} not recognized.")

    def init_conds(self, params: Dict) -> Dict[str, jnp.ndarray]:
        conds = self.init_branch_conds(
            params["axial_resistivity"], params["radius"], params["length"], self.nseg
        )
        cond_params = {
            "branchpoint_conds_children": jnp.asarray([]),
            "branchpoint_conds_parents": jnp.asarray([]),
            "branchpoint_weights_children": jnp.asarray([]),
            "branchpoint_weights_parents": jnp.asarray([]),
        }
        cond_params["branch_lowers"] = conds[0]
        cond_params["branch_uppers"] = conds[1]
        cond_params["branch_diags"] = conds[2]

        return cond_params

    @staticmethod
    def init_branch_conds(
        axial_resistivity: jnp.ndarray,
        radiuses: jnp.ndarray,
        lengths: jnp.ndarray,
        nseg: int,
    ) -> Tuple[jnp.ndarray, jnp.ndarray, jnp.ndarray]:
        """Given an axial resisitivity, set the coupling conductances.

        Args:
            axial_resistivity: Axial resistivity of each compartment.
            radiuses: Radius of each compartment.
            lengths: Length of each compartment.
            nseg: Number of compartments in the branch.

        Returns:
            Tuple of forward coupling conductances, backward coupling conductances, and summed coupling conductances.
        """

        # Compute coupling conductance for segments within a branch.
        # `radius`: um
        # `r_a`: ohm cm
        # `length_single_compartment`: um
        # `coupling_conds`: S * um / cm / um^2 = S / cm / um
        r1 = radiuses[:-1]
        r2 = radiuses[1:]
        r_a1 = axial_resistivity[:-1]
        r_a2 = axial_resistivity[1:]
        l1 = lengths[:-1]
        l2 = lengths[1:]
        coupling_conds_bwd = compute_coupling_cond(r1, r2, r_a1, r_a2, l1, l2)
        coupling_conds_fwd = compute_coupling_cond(r2, r1, r_a2, r_a1, l2, l1)

        # Compute the summed coupling conductances of each compartment.
        summed_coupling_conds = jnp.zeros((nseg))
        summed_coupling_conds = summed_coupling_conds.at[1:].add(coupling_conds_fwd)
        summed_coupling_conds = summed_coupling_conds.at[:-1].add(coupling_conds_bwd)
        return coupling_conds_fwd, coupling_conds_bwd, summed_coupling_conds

    def __len__(self) -> int:
        return self.nseg

__init__(compartments=None, nseg=None)

Parameters:

Name	Type	Description	Default
compartments	Optional[Union[Compartment, List[Compartment]]]	A single compartment or a list of compartments that make up the branch.	None
nseg	Optional[int]	Number of segments to divide the branch into. If compartments is an a single compartment, than the compartment is repeated nseg times to create the branch.	None

Source code in jaxley/modules/branch.py

def __init__(
    self,
    compartments: Optional[Union[Compartment, List[Compartment]]] = None,
    nseg: Optional[int] = None,
):
    """
    Args:
        compartments: A single compartment or a list of compartments that make up the
            branch.
        nseg: Number of segments to divide the branch into. If `compartments` is an
            a single compartment, than the compartment is repeated `nseg` times to
            create the branch.
    """
    super().__init__()
    assert (
        isinstance(compartments, (Compartment, List)) or compartments is None
    ), "Only Compartment or List[Compartment] is allowed."
    if isinstance(compartments, Compartment):
        assert (
            nseg is not None
        ), "If `compartments` is not a list then you have to set `nseg`."
    compartments = Compartment() if compartments is None else compartments
    nseg = 1 if nseg is None else nseg

    if isinstance(compartments, Compartment):
        compartment_list = [compartments] * nseg
    else:
        compartment_list = compartments

    self.nseg = len(compartment_list)
    self.total_nbranches = 1
    self.nbranches_per_cell = [1]
    self.cumsum_nbranches = jnp.asarray([0, 1])

    # Indexing.
    self.nodes = pd.concat([c.nodes for c in compartment_list], ignore_index=True)
    self._append_params_and_states(self.branch_params, self.branch_states)
    self.nodes["comp_index"] = np.arange(self.nseg).tolist()
    self.nodes["branch_index"] = [0] * self.nseg
    self.nodes["cell_index"] = [0] * self.nseg

    # Channels.
    self._gather_channels_from_constituents(compartment_list)

    # Synapse indexing.
    self.syn_edges = pd.DataFrame(
        dict(global_pre_comp_index=[], global_post_comp_index=[], type="")
    )
    self.branch_edges = pd.DataFrame(
        dict(parent_branch_index=[], child_branch_index=[])
    )

    # For morphology indexing.
    self.child_inds = np.asarray([]).astype(int)
    self.child_belongs_to_branchpoint = np.asarray([]).astype(int)
    self.par_inds = np.asarray([]).astype(int)
    self.total_nbranchpoints = 0
    self.branchpoint_group_inds = np.asarray([]).astype(int)

    self.children_in_level = []
    self.parents_in_level = []
    self.root_inds = jnp.asarray([0])

    self.initialize()
    self.init_syns()
    self.initialized_conds = False

    # Coordinates.
    self.xyzr = [float("NaN") * np.zeros((2, 4))]

init_branch_conds(axial_resistivity, radiuses, lengths, nseg) staticmethod

Given an axial resisitivity, set the coupling conductances.

Parameters:

Name	Type	Description	Default
axial_resistivity	ndarray	Axial resistivity of each compartment.	required
radiuses	ndarray	Radius of each compartment.	required
lengths	ndarray	Length of each compartment.	required
nseg	int	Number of compartments in the branch.	required

Returns:

Type	Description
Tuple[ndarray, ndarray, ndarray]	Tuple of forward coupling conductances, backward coupling conductances, and summed coupling conductances.

Source code in jaxley/modules/branch.py

@staticmethod
def init_branch_conds(
    axial_resistivity: jnp.ndarray,
    radiuses: jnp.ndarray,
    lengths: jnp.ndarray,
    nseg: int,
) -> Tuple[jnp.ndarray, jnp.ndarray, jnp.ndarray]:
    """Given an axial resisitivity, set the coupling conductances.

    Args:
        axial_resistivity: Axial resistivity of each compartment.
        radiuses: Radius of each compartment.
        lengths: Length of each compartment.
        nseg: Number of compartments in the branch.

    Returns:
        Tuple of forward coupling conductances, backward coupling conductances, and summed coupling conductances.
    """

    # Compute coupling conductance for segments within a branch.
    # `radius`: um
    # `r_a`: ohm cm
    # `length_single_compartment`: um
    # `coupling_conds`: S * um / cm / um^2 = S / cm / um
    r1 = radiuses[:-1]
    r2 = radiuses[1:]
    r_a1 = axial_resistivity[:-1]
    r_a2 = axial_resistivity[1:]
    l1 = lengths[:-1]
    l2 = lengths[1:]
    coupling_conds_bwd = compute_coupling_cond(r1, r2, r_a1, r_a2, l1, l2)
    coupling_conds_fwd = compute_coupling_cond(r2, r1, r_a2, r_a1, l2, l1)

    # Compute the summed coupling conductances of each compartment.
    summed_coupling_conds = jnp.zeros((nseg))
    summed_coupling_conds = summed_coupling_conds.at[1:].add(coupling_conds_fwd)
    summed_coupling_conds = summed_coupling_conds.at[:-1].add(coupling_conds_bwd)
    return coupling_conds_fwd, coupling_conds_bwd, summed_coupling_conds

Cell

Bases: Module

Cell class.

This class defines a single cell that can be simulated by itself or connected with synapses to build a network. A cell is made up of several branches and supports intricate cell morphologies.

Source code in jaxley/modules/cell.py

class Cell(Module):
    """Cell class.

    This class defines a single cell that can be simulated by itself or
    connected with synapses to build a network. A cell is made up of several branches
    and supports intricate cell morphologies.
    """

    cell_params: Dict = {}
    cell_states: Dict = {}

    def __init__(
        self,
        branches: Optional[Union[Branch, List[Branch]]] = None,
        parents: Optional[List[int]] = None,
        xyzr: Optional[List[np.ndarray]] = None,
    ):
        """Initialize a cell.

        Args:
            branches: A single branch or a list of branches that make up the cell.
                If a single branch is provided, then the branch is repeated `len(parents)`
                times to create the cell.
            parents: The parent branch index for each branch. The first branch has no
                parent and is therefore set to -1.
            xyzr: For every branch, the x, y, and z coordinates and the radius at the
                traced coordinates. Note that this is the full tracing (from SWC), not
                the stick representation coordinates.
        """
        super().__init__()
        assert (
            isinstance(branches, (Branch, List)) or branches is None
        ), "Only Branch or List[Branch] is allowed."
        if branches is not None:
            assert (
                parents is not None
            ), "If `branches` is not a list then you have to set `parents`."
        if isinstance(branches, List):
            assert len(parents) == len(
                branches
            ), "Ensure equally many parents, i.e. len(branches) == len(parents)."

        branches = Branch() if branches is None else branches
        parents = [-1] if parents is None else parents

        if isinstance(branches, Branch):
            branch_list = [branches for _ in range(len(parents))]
        else:
            branch_list = branches

        if xyzr is not None:
            assert len(xyzr) == len(parents)
            self.xyzr = xyzr
        else:
            # For every branch (`len(parents)`), we have a start and end point (`2`) and
            # a (x,y,z,r) coordinate for each of them (`4`).
            # Since `xyzr` is only inspected at `.vis()` and because it depends on the
            # (potentially learned) length of every compartment, we only populate
            # self.xyzr at `.vis()`.
            self.xyzr = [float("NaN") * np.zeros((2, 4)) for _ in range(len(parents))]

        self.nseg = branch_list[0].nseg
        self.total_nbranches = len(branch_list)
        self.nbranches_per_cell = [len(branch_list)]
        self.comb_parents = jnp.asarray(parents)
        self.comb_children = compute_children_indices(self.comb_parents)
        self.cumsum_nbranches = jnp.asarray([0, len(branch_list)])

        # Indexing.
        self.nodes = pd.concat([c.nodes for c in branch_list], ignore_index=True)
        self._append_params_and_states(self.cell_params, self.cell_states)
        self.nodes["comp_index"] = np.arange(self.nseg * self.total_nbranches).tolist()
        self.nodes["branch_index"] = (
            np.arange(self.nseg * self.total_nbranches) // self.nseg
        ).tolist()
        self.nodes["cell_index"] = [0] * (self.nseg * self.total_nbranches)

        # Channels.
        self._gather_channels_from_constituents(branch_list)

        # Synapse indexing.
        self.syn_edges = pd.DataFrame(
            dict(global_pre_comp_index=[], global_post_comp_index=[], type="")
        )
        self.branch_edges = pd.DataFrame(
            dict(
                parent_branch_index=self.comb_parents[1:],
                child_branch_index=np.arange(1, self.total_nbranches),
            )
        )

        # For morphology indexing.
        par_inds = self.branch_edges["parent_branch_index"].to_numpy()
        self.child_inds = self.branch_edges["child_branch_index"].to_numpy()
        self.child_belongs_to_branchpoint = remap_to_consecutive(par_inds)

        # TODO: does order have to be preserved?
        self.par_inds = np.unique(par_inds)
        self.total_nbranchpoints = len(self.par_inds)
        self.root_inds = jnp.asarray([0])

        self.initialize()

        self.init_syns()
        self.initialized_conds = False

    def __getattr__(self, key: str):
        # Ensure that hidden methods such as `__deepcopy__` still work.
        if key.startswith("__"):
            return super().__getattribute__(key)

        if key == "branch":
            view = deepcopy(self.nodes)
            view["global_comp_index"] = view["comp_index"]
            view["global_branch_index"] = view["branch_index"]
            view["global_cell_index"] = view["cell_index"]
            return BranchView(self, view)
        elif key in self.group_nodes:
            inds = self.group_nodes[key].index.values
            view = self.nodes.loc[inds]
            view["global_comp_index"] = view["comp_index"]
            view["global_branch_index"] = view["branch_index"]
            view["global_cell_index"] = view["cell_index"]
            return GroupView(self, view, BranchView, ["branch"])
        else:
            raise KeyError(f"Key {key} not recognized.")

    def init_morph(self):
        """Initialize morphology."""

        # For Jaxley custom implementation.
        children_and_parents = compute_morphology_indices_in_levels(
            len(self.par_inds),
            self.child_belongs_to_branchpoint,
            self.par_inds,
            self.child_inds,
        )
        self.branchpoint_group_inds = build_branchpoint_group_inds(
            len(self.par_inds),
            self.child_belongs_to_branchpoint,
            self.nseg,
            self.total_nbranches,
        )
        parents = self.comb_parents
        children_inds = children_and_parents["children"]
        parents_inds = children_and_parents["parents"]

        levels = compute_levels(parents)
        self.children_in_level = compute_children_in_level(levels, children_inds)
        self.parents_in_level = compute_parents_in_level(
            levels, self.par_inds, parents_inds
        )

        self.initialized_morph = True

    def init_conds(self, params: Dict) -> Dict[str, jnp.ndarray]:
        """Given an axial resisitivity, set the coupling conductances."""
        nbranches = self.total_nbranches
        nseg = self.nseg

        axial_resistivity = jnp.reshape(params["axial_resistivity"], (nbranches, nseg))
        radiuses = jnp.reshape(params["radius"], (nbranches, nseg))
        lengths = jnp.reshape(params["length"], (nbranches, nseg))

        conds = vmap(Branch.init_branch_conds, in_axes=(0, 0, 0, None))(
            axial_resistivity, radiuses, lengths, self.nseg
        )
        coupling_conds_fwd = conds[0]
        coupling_conds_bwd = conds[1]
        summed_coupling_conds = conds[2]

        # The conductance from the children to the branch point.
        branchpoint_conds_children = vmap(
            compute_coupling_cond_branchpoint, in_axes=(0, 0, 0)
        )(
            radiuses[self.child_inds, 0],
            axial_resistivity[self.child_inds, 0],
            lengths[self.child_inds, 0],
        )
        # The conductance from the parents to the branch point.
        branchpoint_conds_parents = vmap(
            compute_coupling_cond_branchpoint, in_axes=(0, 0, 0)
        )(
            radiuses[self.par_inds, -1],
            axial_resistivity[self.par_inds, -1],
            lengths[self.par_inds, -1],
        )

        # Weights with which the compartments influence their nearby node.
        # The impact of the children on the branch point.
        branchpoint_weights_children = vmap(compute_impact_on_node, in_axes=(0, 0, 0))(
            radiuses[self.child_inds, 0],
            axial_resistivity[self.child_inds, 0],
            lengths[self.child_inds, 0],
        )
        # The impact of parents on the branch point.
        branchpoint_weights_parents = vmap(compute_impact_on_node, in_axes=(0, 0, 0))(
            radiuses[self.par_inds, -1],
            axial_resistivity[self.par_inds, -1],
            lengths[self.par_inds, -1],
        )

        summed_coupling_conds = self.update_summed_coupling_conds(
            summed_coupling_conds,
            self.child_inds,
            self.par_inds,
            branchpoint_conds_children,
            branchpoint_conds_parents,
        )

        cond_params = {
            "branch_uppers": coupling_conds_bwd,
            "branch_lowers": coupling_conds_fwd,
            "branch_diags": summed_coupling_conds,
            "branchpoint_conds_children": branchpoint_conds_children,
            "branchpoint_conds_parents": branchpoint_conds_parents,
            "branchpoint_weights_children": branchpoint_weights_children,
            "branchpoint_weights_parents": branchpoint_weights_parents,
        }
        return cond_params

    @staticmethod
    def update_summed_coupling_conds(
        summed_conds,
        child_inds,
        par_inds,
        branchpoint_conds_children,
        branchpoint_conds_parents,
    ):
        """Perform updates on the diagonal based on conductances of the branchpoints.

        Args:
            summed_conds: shape [num_branches, nseg]
            child_inds: shape [num_branches - 1]
            conds_fwd: shape [num_branches - 1]
            conds_bwd: shape [num_branches - 1]
            parents: shape [num_branches]

        Returns:
            Updated `summed_coupling_conds`.
        """
        summed_conds = summed_conds.at[child_inds, 0].add(branchpoint_conds_children)
        summed_conds = summed_conds.at[par_inds, -1].add(branchpoint_conds_parents)
        return summed_conds

__init__(branches=None, parents=None, xyzr=None)

Initialize a cell.

Parameters:

Name	Type	Description	Default
branches	Optional[Union[Branch, List[Branch]]]	A single branch or a list of branches that make up the cell. If a single branch is provided, then the branch is repeated len(parents) times to create the cell.	None
parents	Optional[List[int]]	The parent branch index for each branch. The first branch has no parent and is therefore set to -1.	None
xyzr	Optional[List[ndarray]]	For every branch, the x, y, and z coordinates and the radius at the traced coordinates. Note that this is the full tracing (from SWC), not the stick representation coordinates.	None

Source code in jaxley/modules/cell.py

def __init__(
    self,
    branches: Optional[Union[Branch, List[Branch]]] = None,
    parents: Optional[List[int]] = None,
    xyzr: Optional[List[np.ndarray]] = None,
):
    """Initialize a cell.

    Args:
        branches: A single branch or a list of branches that make up the cell.
            If a single branch is provided, then the branch is repeated `len(parents)`
            times to create the cell.
        parents: The parent branch index for each branch. The first branch has no
            parent and is therefore set to -1.
        xyzr: For every branch, the x, y, and z coordinates and the radius at the
            traced coordinates. Note that this is the full tracing (from SWC), not
            the stick representation coordinates.
    """
    super().__init__()
    assert (
        isinstance(branches, (Branch, List)) or branches is None
    ), "Only Branch or List[Branch] is allowed."
    if branches is not None:
        assert (
            parents is not None
        ), "If `branches` is not a list then you have to set `parents`."
    if isinstance(branches, List):
        assert len(parents) == len(
            branches
        ), "Ensure equally many parents, i.e. len(branches) == len(parents)."

    branches = Branch() if branches is None else branches
    parents = [-1] if parents is None else parents

    if isinstance(branches, Branch):
        branch_list = [branches for _ in range(len(parents))]
    else:
        branch_list = branches

    if xyzr is not None:
        assert len(xyzr) == len(parents)
        self.xyzr = xyzr
    else:
        # For every branch (`len(parents)`), we have a start and end point (`2`) and
        # a (x,y,z,r) coordinate for each of them (`4`).
        # Since `xyzr` is only inspected at `.vis()` and because it depends on the
        # (potentially learned) length of every compartment, we only populate
        # self.xyzr at `.vis()`.
        self.xyzr = [float("NaN") * np.zeros((2, 4)) for _ in range(len(parents))]

    self.nseg = branch_list[0].nseg
    self.total_nbranches = len(branch_list)
    self.nbranches_per_cell = [len(branch_list)]
    self.comb_parents = jnp.asarray(parents)
    self.comb_children = compute_children_indices(self.comb_parents)
    self.cumsum_nbranches = jnp.asarray([0, len(branch_list)])

    # Indexing.
    self.nodes = pd.concat([c.nodes for c in branch_list], ignore_index=True)
    self._append_params_and_states(self.cell_params, self.cell_states)
    self.nodes["comp_index"] = np.arange(self.nseg * self.total_nbranches).tolist()
    self.nodes["branch_index"] = (
        np.arange(self.nseg * self.total_nbranches) // self.nseg
    ).tolist()
    self.nodes["cell_index"] = [0] * (self.nseg * self.total_nbranches)

    # Channels.
    self._gather_channels_from_constituents(branch_list)

    # Synapse indexing.
    self.syn_edges = pd.DataFrame(
        dict(global_pre_comp_index=[], global_post_comp_index=[], type="")
    )
    self.branch_edges = pd.DataFrame(
        dict(
            parent_branch_index=self.comb_parents[1:],
            child_branch_index=np.arange(1, self.total_nbranches),
        )
    )

    # For morphology indexing.
    par_inds = self.branch_edges["parent_branch_index"].to_numpy()
    self.child_inds = self.branch_edges["child_branch_index"].to_numpy()
    self.child_belongs_to_branchpoint = remap_to_consecutive(par_inds)

    # TODO: does order have to be preserved?
    self.par_inds = np.unique(par_inds)
    self.total_nbranchpoints = len(self.par_inds)
    self.root_inds = jnp.asarray([0])

    self.initialize()

    self.init_syns()
    self.initialized_conds = False

init_conds(params)

Given an axial resisitivity, set the coupling conductances.

Source code in jaxley/modules/cell.py

def init_conds(self, params: Dict) -> Dict[str, jnp.ndarray]:
    """Given an axial resisitivity, set the coupling conductances."""
    nbranches = self.total_nbranches
    nseg = self.nseg

    axial_resistivity = jnp.reshape(params["axial_resistivity"], (nbranches, nseg))
    radiuses = jnp.reshape(params["radius"], (nbranches, nseg))
    lengths = jnp.reshape(params["length"], (nbranches, nseg))

    conds = vmap(Branch.init_branch_conds, in_axes=(0, 0, 0, None))(
        axial_resistivity, radiuses, lengths, self.nseg
    )
    coupling_conds_fwd = conds[0]
    coupling_conds_bwd = conds[1]
    summed_coupling_conds = conds[2]

    # The conductance from the children to the branch point.
    branchpoint_conds_children = vmap(
        compute_coupling_cond_branchpoint, in_axes=(0, 0, 0)
    )(
        radiuses[self.child_inds, 0],
        axial_resistivity[self.child_inds, 0],
        lengths[self.child_inds, 0],
    )
    # The conductance from the parents to the branch point.
    branchpoint_conds_parents = vmap(
        compute_coupling_cond_branchpoint, in_axes=(0, 0, 0)
    )(
        radiuses[self.par_inds, -1],
        axial_resistivity[self.par_inds, -1],
        lengths[self.par_inds, -1],
    )

    # Weights with which the compartments influence their nearby node.
    # The impact of the children on the branch point.
    branchpoint_weights_children = vmap(compute_impact_on_node, in_axes=(0, 0, 0))(
        radiuses[self.child_inds, 0],
        axial_resistivity[self.child_inds, 0],
        lengths[self.child_inds, 0],
    )
    # The impact of parents on the branch point.
    branchpoint_weights_parents = vmap(compute_impact_on_node, in_axes=(0, 0, 0))(
        radiuses[self.par_inds, -1],
        axial_resistivity[self.par_inds, -1],
        lengths[self.par_inds, -1],
    )

    summed_coupling_conds = self.update_summed_coupling_conds(
        summed_coupling_conds,
        self.child_inds,
        self.par_inds,
        branchpoint_conds_children,
        branchpoint_conds_parents,
    )

    cond_params = {
        "branch_uppers": coupling_conds_bwd,
        "branch_lowers": coupling_conds_fwd,
        "branch_diags": summed_coupling_conds,
        "branchpoint_conds_children": branchpoint_conds_children,
        "branchpoint_conds_parents": branchpoint_conds_parents,
        "branchpoint_weights_children": branchpoint_weights_children,
        "branchpoint_weights_parents": branchpoint_weights_parents,
    }
    return cond_params

init_morph()

Initialize morphology.

Source code in jaxley/modules/cell.py

def init_morph(self):
    """Initialize morphology."""

    # For Jaxley custom implementation.
    children_and_parents = compute_morphology_indices_in_levels(
        len(self.par_inds),
        self.child_belongs_to_branchpoint,
        self.par_inds,
        self.child_inds,
    )
    self.branchpoint_group_inds = build_branchpoint_group_inds(
        len(self.par_inds),
        self.child_belongs_to_branchpoint,
        self.nseg,
        self.total_nbranches,
    )
    parents = self.comb_parents
    children_inds = children_and_parents["children"]
    parents_inds = children_and_parents["parents"]

    levels = compute_levels(parents)
    self.children_in_level = compute_children_in_level(levels, children_inds)
    self.parents_in_level = compute_parents_in_level(
        levels, self.par_inds, parents_inds
    )

    self.initialized_morph = True

update_summed_coupling_conds(summed_conds, child_inds, par_inds, branchpoint_conds_children, branchpoint_conds_parents) staticmethod

Perform updates on the diagonal based on conductances of the branchpoints.

Parameters:

Name	Type	Description	Default
summed_conds		shape [num_branches, nseg]	required
child_inds		shape [num_branches - 1]	required
conds_fwd		shape [num_branches - 1]	required
conds_bwd		shape [num_branches - 1]	required
parents		shape [num_branches]	required

Returns:

Type	Description
	Updated summed_coupling_conds.

Source code in jaxley/modules/cell.py

@staticmethod
def update_summed_coupling_conds(
    summed_conds,
    child_inds,
    par_inds,
    branchpoint_conds_children,
    branchpoint_conds_parents,
):
    """Perform updates on the diagonal based on conductances of the branchpoints.

    Args:
        summed_conds: shape [num_branches, nseg]
        child_inds: shape [num_branches - 1]
        conds_fwd: shape [num_branches - 1]
        conds_bwd: shape [num_branches - 1]
        parents: shape [num_branches]

    Returns:
        Updated `summed_coupling_conds`.
    """
    summed_conds = summed_conds.at[child_inds, 0].add(branchpoint_conds_children)
    summed_conds = summed_conds.at[par_inds, -1].add(branchpoint_conds_parents)
    return summed_conds

Network

Bases: Module

Network class.

This class defines a network of cells that can be connected with synapses.

Source code in jaxley/modules/network.py

class Network(Module):
    """Network class.

    This class defines a network of cells that can be connected with synapses.
    """

    network_params: Dict = {}
    network_states: Dict = {}

    def __init__(
        self,
        cells: List[Cell],
    ):
        """Initialize network of cells and synapses.

        Args:
            cells: A list of cells that make up the network.
        """
        super().__init__()
        for cell in cells:
            self.xyzr += deepcopy(cell.xyzr)

        self.cells = cells
        self.nseg = cells[0].nseg
        self._append_params_and_states(self.network_params, self.network_states)

        self.nbranches_per_cell = [cell.total_nbranches for cell in self.cells]
        self.nbranchpoints_per_cell = [cell.total_nbranchpoints for cell in self.cells]
        self.total_nbranches = sum(self.nbranches_per_cell)
        self.cumsum_nbranches = jnp.cumsum(jnp.asarray([0] + self.nbranches_per_cell))
        self.cumsum_nbranchpoints = jnp.cumsum(
            jnp.asarray([0] + self.nbranchpoints_per_cell)
        )

        self.nodes = pd.concat([c.nodes for c in cells], ignore_index=True)
        self.nodes["comp_index"] = np.arange(self.nseg * self.total_nbranches).tolist()
        self.nodes["branch_index"] = (
            np.arange(self.nseg * self.total_nbranches) // self.nseg
        ).tolist()
        self.nodes["cell_index"] = list(
            itertools.chain(
                *[[i] * (self.nseg * b) for i, b in enumerate(self.nbranches_per_cell)]
            )
        )

        parents = [cell.comb_parents for cell in self.cells]
        self.comb_parents = jnp.concatenate(
            [p.at[1:].add(self.cumsum_nbranches[i]) for i, p in enumerate(parents)]
        )

        # Two columns: `parent_branch_index` and `child_branch_index`. One row per
        # branch, apart from those branches which do not have a parent (i.e.
        # -1 in parents). For every branch, tracks the global index of that branch
        # (`child_branch_index`) and the global index of its parent
        # (`parent_branch_index`).
        self.branch_edges = pd.DataFrame(
            dict(
                parent_branch_index=self.comb_parents[self.comb_parents != -1],
                child_branch_index=np.where(self.comb_parents != -1)[0],
            )
        )

        # For morphology indexing.
        par_inds = self.branch_edges["parent_branch_index"].to_numpy()
        self.child_inds = self.branch_edges["child_branch_index"].to_numpy()
        self.child_belongs_to_branchpoint = remap_to_consecutive(par_inds)
        self.par_inds = np.unique(par_inds)  # TODO: does order have to be preserved?
        self.total_nbranchpoints = len(self.par_inds)
        self.root_inds = self.cumsum_nbranches[:-1]

        # Channels.
        self._gather_channels_from_constituents(cells)

        self.initialize()
        self.init_syns()
        self.initialized_conds = False

    def __getattr__(self, key: str):
        # Ensure that hidden methods such as `__deepcopy__` still work.
        if key.startswith("__"):
            return super().__getattribute__(key)

        if key == "cell":
            view = deepcopy(self.nodes)
            view["global_comp_index"] = view["comp_index"]
            view["global_branch_index"] = view["branch_index"]
            view["global_cell_index"] = view["cell_index"]
            return CellView(self, view)
        elif key in self.synapse_names:
            type_index = self.synapse_names.index(key)
            return SynapseView(self, self.edges, key, self.synapses[type_index])
        elif key in self.group_nodes:
            inds = self.group_nodes[key].index.values
            view = self.nodes.loc[inds]
            view["global_comp_index"] = view["comp_index"]
            view["global_branch_index"] = view["branch_index"]
            view["global_cell_index"] = view["cell_index"]
            return GroupView(self, view, CellView, ["cell"])
        else:
            raise KeyError(f"Key {key} not recognized.")

    def init_morph(self):
        self.branchpoint_group_inds = build_branchpoint_group_inds(
            len(self.par_inds),
            self.child_belongs_to_branchpoint,
            self.nseg,
            self.total_nbranches,
        )
        self.children_in_level = merge_cells(
            self.cumsum_nbranches,
            self.cumsum_nbranchpoints,
            [cell.children_in_level for cell in self.cells],
            exclude_first=False,
        )
        self.parents_in_level = merge_cells(
            self.cumsum_nbranches,
            self.cumsum_nbranchpoints,
            [cell.parents_in_level for cell in self.cells],
            exclude_first=False,
        )
        self.initialized_morph = True

    def init_conds(self, params: Dict) -> Dict[str, jnp.ndarray]:
        """Given an axial resisitivity, set the coupling conductances."""
        nbranches = self.total_nbranches
        nseg = self.nseg
        parents = self.comb_parents

        axial_resistivity = jnp.reshape(params["axial_resistivity"], (nbranches, nseg))
        radiuses = jnp.reshape(params["radius"], (nbranches, nseg))
        lengths = jnp.reshape(params["length"], (nbranches, nseg))

        conds = vmap(Branch.init_branch_conds, in_axes=(0, 0, 0, None))(
            axial_resistivity, radiuses, lengths, self.nseg
        )
        coupling_conds_fwd = conds[0]
        coupling_conds_bwd = conds[1]
        summed_coupling_conds = conds[2]

        # The conductance from the children to the branch point.
        branchpoint_conds_children = vmap(
            compute_coupling_cond_branchpoint, in_axes=(0, 0, 0)
        )(
            radiuses[self.child_inds, 0],
            axial_resistivity[self.child_inds, 0],
            lengths[self.child_inds, 0],
        )
        # The conductance from the parents to the branch point.
        branchpoint_conds_parents = vmap(
            compute_coupling_cond_branchpoint, in_axes=(0, 0, 0)
        )(
            radiuses[self.par_inds, -1],
            axial_resistivity[self.par_inds, -1],
            lengths[self.par_inds, -1],
        )

        # Weights with which the compartments influence their nearby node.
        # The impact of the children on the branch point.
        branchpoint_weights_children = vmap(compute_impact_on_node, in_axes=(0, 0, 0))(
            radiuses[self.child_inds, 0],
            axial_resistivity[self.child_inds, 0],
            lengths[self.child_inds, 0],
        )
        # The impact of parents on the branch point.
        branchpoint_weights_parents = vmap(compute_impact_on_node, in_axes=(0, 0, 0))(
            radiuses[self.par_inds, -1],
            axial_resistivity[self.par_inds, -1],
            lengths[self.par_inds, -1],
        )

        summed_coupling_conds = Cell.update_summed_coupling_conds(
            summed_coupling_conds,
            self.child_inds,
            self.par_inds,
            branchpoint_conds_children,
            branchpoint_conds_parents,
        )

        cond_params = {
            "branch_uppers": coupling_conds_bwd,
            "branch_lowers": coupling_conds_fwd,
            "branch_diags": summed_coupling_conds,
            "branchpoint_conds_children": branchpoint_conds_children,
            "branchpoint_conds_parents": branchpoint_conds_parents,
            "branchpoint_weights_children": branchpoint_weights_children,
            "branchpoint_weights_parents": branchpoint_weights_parents,
        }
        return cond_params

    def init_syns(self):
        """Initialize synapses."""
        self.synapses = []

        # TODO(@michaeldeistler): should we also track this for channels?
        self.synapse_names = []
        self.synapse_param_names = []
        self.synapse_state_names = []

        self.initialized_syns = True

    def _step_synapse(
        self,
        states: Dict,
        syn_channels: List,
        params: Dict,
        delta_t: float,
        edges: pd.DataFrame,
    ) -> Tuple[Dict, Tuple[jnp.ndarray, jnp.ndarray]]:
        """Perform one step of the synapses and obtain their currents."""
        states = self._step_synapse_state(states, syn_channels, params, delta_t, edges)
        states, current_terms = self._synapse_currents(
            states, syn_channels, params, delta_t, edges
        )
        return states, current_terms

    def _step_synapse_state(
        self,
        states: Dict,
        syn_channels: List,
        params: Dict,
        delta_t: float,
        edges: pd.DataFrame,
    ) -> Dict:
        voltages = states["v"]

        grouped_syns = edges.groupby("type", sort=False, group_keys=False)
        pre_syn_inds = grouped_syns["global_pre_comp_index"].apply(list)
        post_syn_inds = grouped_syns["global_post_comp_index"].apply(list)
        synapse_names = list(grouped_syns.indices.keys())

        for i, synapse_type in enumerate(syn_channels):
            assert (
                synapse_names[i] == synapse_type._name
            ), "Mixup in the ordering of synapses. Please create an issue on Github."
            synapse_param_names = list(synapse_type.synapse_params.keys())
            synapse_state_names = list(synapse_type.synapse_states.keys())

            synapse_params = {}
            for p in synapse_param_names:
                synapse_params[p] = params[p]
            synapse_states = {}
            for s in synapse_state_names:
                synapse_states[s] = states[s]

            pre_inds = np.asarray(pre_syn_inds[synapse_names[i]])
            post_inds = np.asarray(post_syn_inds[synapse_names[i]])

            # State updates.
            states_updated = synapse_type.update_states(
                synapse_states,
                delta_t,
                voltages[pre_inds],
                voltages[post_inds],
                synapse_params,
            )

            # Rebuild state.
            for key, val in states_updated.items():
                states[key] = val

        return states

    def _synapse_currents(
        self,
        states: Dict,
        syn_channels: List,
        params: Dict,
        delta_t: float,
        edges: pd.DataFrame,
    ) -> Tuple[Dict, Tuple[jnp.ndarray, jnp.ndarray]]:
        voltages = states["v"]

        grouped_syns = edges.groupby("type", sort=False, group_keys=False)
        pre_syn_inds = grouped_syns["global_pre_comp_index"].apply(list)
        post_syn_inds = grouped_syns["global_post_comp_index"].apply(list)
        synapse_names = list(grouped_syns.indices.keys())

        syn_voltage_terms = jnp.zeros_like(voltages)
        syn_constant_terms = jnp.zeros_like(voltages)
        # Run with two different voltages that are `diff` apart to infer the slope and
        # offset.
        diff = 1e-3
        for i, synapse_type in enumerate(syn_channels):
            assert (
                synapse_names[i] == synapse_type._name
            ), "Mixup in the ordering of synapses. Please create an issue on Github."
            synapse_param_names = list(synapse_type.synapse_params.keys())
            synapse_state_names = list(synapse_type.synapse_states.keys())

            synapse_params = {}
            for p in synapse_param_names:
                synapse_params[p] = params[p]
            synapse_states = {}
            for s in synapse_state_names:
                synapse_states[s] = states[s]

            # Get pre and post indexes of the current synapse type.
            pre_inds = np.asarray(pre_syn_inds[synapse_names[i]])
            post_inds = np.asarray(post_syn_inds[synapse_names[i]])

            # Compute slope and offset of the current through every synapse.
            pre_v_and_perturbed = jnp.stack(
                [voltages[pre_inds], voltages[pre_inds] + diff]
            )
            post_v_and_perturbed = jnp.stack(
                [voltages[post_inds], voltages[post_inds] + diff]
            )
            synapse_currents = vmap(
                synapse_type.compute_current, in_axes=(None, 0, 0, None)
            )(
                synapse_states,
                pre_v_and_perturbed,
                post_v_and_perturbed,
                synapse_params,
            )
            synapse_currents_dist = convert_point_process_to_distributed(
                synapse_currents,
                params["radius"][post_inds],
                params["length"][post_inds],
            )

            # Split into voltage and constant terms.
            voltage_term = (synapse_currents_dist[1] - synapse_currents_dist[0]) / diff
            constant_term = (
                synapse_currents_dist[0] - voltage_term * voltages[post_inds]
            )

            # Gather slope and offset for every postsynaptic compartment.
            gathered_syn_currents = gather_synapes(
                len(voltages),
                post_inds,
                voltage_term,
                constant_term,
            )
            syn_voltage_terms += gathered_syn_currents[0]
            syn_constant_terms -= gathered_syn_currents[1]

            # Add the synaptic currents through every compartment as state.
            # `post_syn_currents` is a `jnp.ndarray` of as many elements as there are
            # compartments in the network.
            # `[0]` because we only use the non-perturbed voltage.
            states[f"{synapse_type._name}_current"] = synapse_currents[0]

        return states, (syn_voltage_terms, syn_constant_terms)

    def vis(
        self,
        detail: str = "full",
        ax: Optional[Axes] = None,
        col: str = "k",
        synapse_col: str = "b",
        dims: Tuple[int] = (0, 1),
        type: str = "line",
        layers: Optional[List] = None,
        morph_plot_kwargs: Dict = {},
        synapse_plot_kwargs: Dict = {},
        synapse_scatter_kwargs: Dict = {},
        networkx_options: Dict = {},
        layer_kwargs: Dict = {},
    ) -> Axes:
        """Visualize the module.

        Args:
            detail: Either of [point, full]. `point` visualizes every neuron in the
                network as a dot (and it uses `networkx` to obtain cell positions).
                `full` plots the full morphology of every neuron. It requires that
                `compute_xyz()` has been run and allows for indivual neurons to be
                moved with `.move()`.
            col: The color in which cells are plotted. Only takes effect if
                `detail='full'`.
            type: Either `line` or `scatter`. Only takes effect if `detail='full'`.
            synapse_col: The color in which synapses are plotted. Only takes effect if
                `detail='full'`.
            dims: Which dimensions to plot. 1=x, 2=y, 3=z coordinate. Must be a tuple of
                two of them.
            layers: Allows to plot the network in layers. Should provide the number of
                neurons in each layer, e.g., [5, 10, 1] would be a network with 5 input
                neurons, 10 hidden layer neurons, and 1 output neuron.
            morph_plot_kwargs: Keyword arguments passed to the plotting function for
                cell morphologies. Only takes effect for `detail='full'`.
            synapse_plot_kwargs: Keyword arguments passed to the plotting function for
                syanpses. Only takes effect for `detail='full'`.
            synapse_scatter_kwargs: Keyword arguments passed to the scatter function
                for the end point of synapses. Only takes effect for `detail='full'`.
            networkx_options: Options passed to `networkx.draw()`. Only takes effect if
                `detail='point'`.
            layer_kwargs: Only used if `layers` is specified and if `detail='full'`.
                Can have the following entries: `within_layer_offset` (float),
                `between_layer_offset` (float), `vertical_layers` (bool).
        """
        if detail == "point":
            graph = self._build_graph(layers)

            if layers is not None:
                pos = nx.multipartite_layout(graph, subset_key="layer")
                nx.draw(graph, pos, with_labels=True, **networkx_options)
            else:
                nx.draw(graph, with_labels=True, **networkx_options)
        elif detail == "full":
            if layers is not None:
                # Assemble cells in the network into layers.
                global_counter = 0
                layers_config = {
                    "within_layer_offset": 500.0,
                    "between_layer_offset": 1500.0,
                    "vertical_layers": False,
                }
                layers_config.update(layer_kwargs)
                for layer_ind, num_in_layer in enumerate(layers):
                    for ind_within_layer in range(num_in_layer):
                        if layers_config["vertical_layers"]:
                            x_offset = (
                                ind_within_layer - (num_in_layer - 1) / 2
                            ) * layers_config["within_layer_offset"]
                            y_offset = (len(layers) - 1 - layer_ind) * layers_config[
                                "between_layer_offset"
                            ]
                        else:
                            x_offset = layer_ind * layers_config["between_layer_offset"]
                            y_offset = (
                                ind_within_layer - (num_in_layer - 1) / 2
                            ) * layers_config["within_layer_offset"]

                        self.cell(global_counter).move_to(x=x_offset, y=y_offset, z=0)
                        global_counter += 1
            ax = self._vis(
                dims=dims,
                col=col,
                ax=ax,
                type=type,
                view=self.nodes,
                morph_plot_kwargs=morph_plot_kwargs,
            )

            pre_locs = self.edges["pre_locs"].to_numpy()
            post_locs = self.edges["post_locs"].to_numpy()
            pre_branch = self.edges["global_pre_branch_index"].to_numpy()
            post_branch = self.edges["global_post_branch_index"].to_numpy()

            dims_np = np.asarray(dims)

            for pre_loc, post_loc, pre_b, post_b in zip(
                pre_locs, post_locs, pre_branch, post_branch
            ):
                pre_coord = self.xyzr[pre_b]
                if len(pre_coord) == 2:
                    # If only start and end point of a branch are traced, perform a
                    # linear interpolation to get the synpase location.
                    pre_coord = pre_coord[0] + (pre_coord[1] - pre_coord[0]) * pre_loc
                else:
                    # If densely traced, use intermediate trace values for synapse loc.
                    middle_ind = int((len(pre_coord) - 1) * pre_loc)
                    pre_coord = pre_coord[middle_ind]

                post_coord = self.xyzr[post_b]
                if len(post_coord) == 2:
                    # If only start and end point of a branch are traced, perform a
                    # linear interpolation to get the synpase location.
                    post_coord = (
                        post_coord[0] + (post_coord[1] - post_coord[0]) * post_loc
                    )
                else:
                    # If densely traced, use intermediate trace values for synapse loc.
                    middle_ind = int((len(post_coord) - 1) * post_loc)
                    post_coord = post_coord[middle_ind]

                coords = np.stack([pre_coord[dims_np], post_coord[dims_np]]).T
                ax.plot(
                    coords[0],
                    coords[1],
                    c=synapse_col,
                    **synapse_plot_kwargs,
                )
                ax.scatter(
                    post_coord[dims_np[0]],
                    post_coord[dims_np[1]],
                    c=synapse_col,
                    **synapse_scatter_kwargs,
                )
        else:
            raise ValueError("detail must be in {full, point}.")

        return ax

    def _build_graph(self, layers: Optional[List] = None, **options):
        graph = nx.DiGraph()

        def build_extents(*subset_sizes):
            return nx.utils.pairwise(itertools.accumulate((0,) + subset_sizes))

        if layers is not None:
            extents = build_extents(*layers)
            layers = [range(start, end) for start, end in extents]
            for i, layer in enumerate(layers):
                graph.add_nodes_from(layer, layer=i)
        else:
            graph.add_nodes_from(range(len(self.cells)))

        pre_cell = self.edges["pre_cell_index"].to_numpy()
        post_cell = self.edges["post_cell_index"].to_numpy()

        inds = np.stack([pre_cell, post_cell]).T
        graph.add_edges_from(inds)

        return graph

__init__(cells)

Initialize network of cells and synapses.

Parameters:

Name	Type	Description	Default
cells	List[Cell]	A list of cells that make up the network.	required

Source code in jaxley/modules/network.py

def __init__(
    self,
    cells: List[Cell],
):
    """Initialize network of cells and synapses.

    Args:
        cells: A list of cells that make up the network.
    """
    super().__init__()
    for cell in cells:
        self.xyzr += deepcopy(cell.xyzr)

    self.cells = cells
    self.nseg = cells[0].nseg
    self._append_params_and_states(self.network_params, self.network_states)

    self.nbranches_per_cell = [cell.total_nbranches for cell in self.cells]
    self.nbranchpoints_per_cell = [cell.total_nbranchpoints for cell in self.cells]
    self.total_nbranches = sum(self.nbranches_per_cell)
    self.cumsum_nbranches = jnp.cumsum(jnp.asarray([0] + self.nbranches_per_cell))
    self.cumsum_nbranchpoints = jnp.cumsum(
        jnp.asarray([0] + self.nbranchpoints_per_cell)
    )

    self.nodes = pd.concat([c.nodes for c in cells], ignore_index=True)
    self.nodes["comp_index"] = np.arange(self.nseg * self.total_nbranches).tolist()
    self.nodes["branch_index"] = (
        np.arange(self.nseg * self.total_nbranches) // self.nseg
    ).tolist()
    self.nodes["cell_index"] = list(
        itertools.chain(
            *[[i] * (self.nseg * b) for i, b in enumerate(self.nbranches_per_cell)]
        )
    )

    parents = [cell.comb_parents for cell in self.cells]
    self.comb_parents = jnp.concatenate(
        [p.at[1:].add(self.cumsum_nbranches[i]) for i, p in enumerate(parents)]
    )

    # Two columns: `parent_branch_index` and `child_branch_index`. One row per
    # branch, apart from those branches which do not have a parent (i.e.
    # -1 in parents). For every branch, tracks the global index of that branch
    # (`child_branch_index`) and the global index of its parent
    # (`parent_branch_index`).
    self.branch_edges = pd.DataFrame(
        dict(
            parent_branch_index=self.comb_parents[self.comb_parents != -1],
            child_branch_index=np.where(self.comb_parents != -1)[0],
        )
    )

    # For morphology indexing.
    par_inds = self.branch_edges["parent_branch_index"].to_numpy()
    self.child_inds = self.branch_edges["child_branch_index"].to_numpy()
    self.child_belongs_to_branchpoint = remap_to_consecutive(par_inds)
    self.par_inds = np.unique(par_inds)  # TODO: does order have to be preserved?
    self.total_nbranchpoints = len(self.par_inds)
    self.root_inds = self.cumsum_nbranches[:-1]

    # Channels.
    self._gather_channels_from_constituents(cells)

    self.initialize()
    self.init_syns()
    self.initialized_conds = False

init_conds(params)

Given an axial resisitivity, set the coupling conductances.

Source code in jaxley/modules/network.py

def init_conds(self, params: Dict) -> Dict[str, jnp.ndarray]:
    """Given an axial resisitivity, set the coupling conductances."""
    nbranches = self.total_nbranches
    nseg = self.nseg
    parents = self.comb_parents

    axial_resistivity = jnp.reshape(params["axial_resistivity"], (nbranches, nseg))
    radiuses = jnp.reshape(params["radius"], (nbranches, nseg))
    lengths = jnp.reshape(params["length"], (nbranches, nseg))

    conds = vmap(Branch.init_branch_conds, in_axes=(0, 0, 0, None))(
        axial_resistivity, radiuses, lengths, self.nseg
    )
    coupling_conds_fwd = conds[0]
    coupling_conds_bwd = conds[1]
    summed_coupling_conds = conds[2]

    # The conductance from the children to the branch point.
    branchpoint_conds_children = vmap(
        compute_coupling_cond_branchpoint, in_axes=(0, 0, 0)
    )(
        radiuses[self.child_inds, 0],
        axial_resistivity[self.child_inds, 0],
        lengths[self.child_inds, 0],
    )
    # The conductance from the parents to the branch point.
    branchpoint_conds_parents = vmap(
        compute_coupling_cond_branchpoint, in_axes=(0, 0, 0)
    )(
        radiuses[self.par_inds, -1],
        axial_resistivity[self.par_inds, -1],
        lengths[self.par_inds, -1],
    )

    # Weights with which the compartments influence their nearby node.
    # The impact of the children on the branch point.
    branchpoint_weights_children = vmap(compute_impact_on_node, in_axes=(0, 0, 0))(
        radiuses[self.child_inds, 0],
        axial_resistivity[self.child_inds, 0],
        lengths[self.child_inds, 0],
    )
    # The impact of parents on the branch point.
    branchpoint_weights_parents = vmap(compute_impact_on_node, in_axes=(0, 0, 0))(
        radiuses[self.par_inds, -1],
        axial_resistivity[self.par_inds, -1],
        lengths[self.par_inds, -1],
    )

    summed_coupling_conds = Cell.update_summed_coupling_conds(
        summed_coupling_conds,
        self.child_inds,
        self.par_inds,
        branchpoint_conds_children,
        branchpoint_conds_parents,
    )

    cond_params = {
        "branch_uppers": coupling_conds_bwd,
        "branch_lowers": coupling_conds_fwd,
        "branch_diags": summed_coupling_conds,
        "branchpoint_conds_children": branchpoint_conds_children,
        "branchpoint_conds_parents": branchpoint_conds_parents,
        "branchpoint_weights_children": branchpoint_weights_children,
        "branchpoint_weights_parents": branchpoint_weights_parents,
    }
    return cond_params

init_syns()

Initialize synapses.

Source code in jaxley/modules/network.py

def init_syns(self):
    """Initialize synapses."""
    self.synapses = []

    # TODO(@michaeldeistler): should we also track this for channels?
    self.synapse_names = []
    self.synapse_param_names = []
    self.synapse_state_names = []

    self.initialized_syns = True

vis(detail='full', ax=None, col='k', synapse_col='b', dims=(0, 1), type='line', layers=None, morph_plot_kwargs={}, synapse_plot_kwargs={}, synapse_scatter_kwargs={}, networkx_options={}, layer_kwargs={})

Visualize the module.

Parameters:

Name	Type	Description	Default
detail	str	Either of [point, full]. point visualizes every neuron in the network as a dot (and it uses networkx to obtain cell positions). full plots the full morphology of every neuron. It requires that compute_xyz() has been run and allows for indivual neurons to be moved with .move().	'full'
col	str	The color in which cells are plotted. Only takes effect if detail='full'.	'k'
type	str	Either line or scatter. Only takes effect if detail='full'.	'line'
synapse_col	str	The color in which synapses are plotted. Only takes effect if detail='full'.	'b'
dims	Tuple[int]	Which dimensions to plot. 1=x, 2=y, 3=z coordinate. Must be a tuple of two of them.	(0, 1)
layers	Optional[List]	Allows to plot the network in layers. Should provide the number of neurons in each layer, e.g., [5, 10, 1] would be a network with 5 input neurons, 10 hidden layer neurons, and 1 output neuron.	None
morph_plot_kwargs	Dict	Keyword arguments passed to the plotting function for cell morphologies. Only takes effect for detail='full'.	{}
synapse_plot_kwargs	Dict	Keyword arguments passed to the plotting function for syanpses. Only takes effect for detail='full'.	{}
synapse_scatter_kwargs	Dict	Keyword arguments passed to the scatter function for the end point of synapses. Only takes effect for detail='full'.	{}
networkx_options	Dict	Options passed to networkx.draw(). Only takes effect if detail='point'.	{}
layer_kwargs	Dict	Only used if layers is specified and if detail='full'. Can have the following entries: within_layer_offset (float), between_layer_offset (float), vertical_layers (bool).	{}

Source code in jaxley/modules/network.py

def vis(
    self,
    detail: str = "full",
    ax: Optional[Axes] = None,
    col: str = "k",
    synapse_col: str = "b",
    dims: Tuple[int] = (0, 1),
    type: str = "line",
    layers: Optional[List] = None,
    morph_plot_kwargs: Dict = {},
    synapse_plot_kwargs: Dict = {},
    synapse_scatter_kwargs: Dict = {},
    networkx_options: Dict = {},
    layer_kwargs: Dict = {},
) -> Axes:
    """Visualize the module.

    Args:
        detail: Either of [point, full]. `point` visualizes every neuron in the
            network as a dot (and it uses `networkx` to obtain cell positions).
            `full` plots the full morphology of every neuron. It requires that
            `compute_xyz()` has been run and allows for indivual neurons to be
            moved with `.move()`.
        col: The color in which cells are plotted. Only takes effect if
            `detail='full'`.
        type: Either `line` or `scatter`. Only takes effect if `detail='full'`.
        synapse_col: The color in which synapses are plotted. Only takes effect if
            `detail='full'`.
        dims: Which dimensions to plot. 1=x, 2=y, 3=z coordinate. Must be a tuple of
            two of them.
        layers: Allows to plot the network in layers. Should provide the number of
            neurons in each layer, e.g., [5, 10, 1] would be a network with 5 input
            neurons, 10 hidden layer neurons, and 1 output neuron.
        morph_plot_kwargs: Keyword arguments passed to the plotting function for
            cell morphologies. Only takes effect for `detail='full'`.
        synapse_plot_kwargs: Keyword arguments passed to the plotting function for
            syanpses. Only takes effect for `detail='full'`.
        synapse_scatter_kwargs: Keyword arguments passed to the scatter function
            for the end point of synapses. Only takes effect for `detail='full'`.
        networkx_options: Options passed to `networkx.draw()`. Only takes effect if
            `detail='point'`.
        layer_kwargs: Only used if `layers` is specified and if `detail='full'`.
            Can have the following entries: `within_layer_offset` (float),
            `between_layer_offset` (float), `vertical_layers` (bool).
    """
    if detail == "point":
        graph = self._build_graph(layers)

        if layers is not None:
            pos = nx.multipartite_layout(graph, subset_key="layer")
            nx.draw(graph, pos, with_labels=True, **networkx_options)
        else:
            nx.draw(graph, with_labels=True, **networkx_options)
    elif detail == "full":
        if layers is not None:
            # Assemble cells in the network into layers.
            global_counter = 0
            layers_config = {
                "within_layer_offset": 500.0,
                "between_layer_offset": 1500.0,
                "vertical_layers": False,
            }
            layers_config.update(layer_kwargs)
            for layer_ind, num_in_layer in enumerate(layers):
                for ind_within_layer in range(num_in_layer):
                    if layers_config["vertical_layers"]:
                        x_offset = (
                            ind_within_layer - (num_in_layer - 1) / 2
                        ) * layers_config["within_layer_offset"]
                        y_offset = (len(layers) - 1 - layer_ind) * layers_config[
                            "between_layer_offset"
                        ]
                    else:
                        x_offset = layer_ind * layers_config["between_layer_offset"]
                        y_offset = (
                            ind_within_layer - (num_in_layer - 1) / 2
                        ) * layers_config["within_layer_offset"]

                    self.cell(global_counter).move_to(x=x_offset, y=y_offset, z=0)
                    global_counter += 1
        ax = self._vis(
            dims=dims,
            col=col,
            ax=ax,
            type=type,
            view=self.nodes,
            morph_plot_kwargs=morph_plot_kwargs,
        )

        pre_locs = self.edges["pre_locs"].to_numpy()
        post_locs = self.edges["post_locs"].to_numpy()
        pre_branch = self.edges["global_pre_branch_index"].to_numpy()
        post_branch = self.edges["global_post_branch_index"].to_numpy()

        dims_np = np.asarray(dims)

        for pre_loc, post_loc, pre_b, post_b in zip(
            pre_locs, post_locs, pre_branch, post_branch
        ):
            pre_coord = self.xyzr[pre_b]
            if len(pre_coord) == 2:
                # If only start and end point of a branch are traced, perform a
                # linear interpolation to get the synpase location.
                pre_coord = pre_coord[0] + (pre_coord[1] - pre_coord[0]) * pre_loc
            else:
                # If densely traced, use intermediate trace values for synapse loc.
                middle_ind = int((len(pre_coord) - 1) * pre_loc)
                pre_coord = pre_coord[middle_ind]

            post_coord = self.xyzr[post_b]
            if len(post_coord) == 2:
                # If only start and end point of a branch are traced, perform a
                # linear interpolation to get the synpase location.
                post_coord = (
                    post_coord[0] + (post_coord[1] - post_coord[0]) * post_loc
                )
            else:
                # If densely traced, use intermediate trace values for synapse loc.
                middle_ind = int((len(post_coord) - 1) * post_loc)
                post_coord = post_coord[middle_ind]

            coords = np.stack([pre_coord[dims_np], post_coord[dims_np]]).T
            ax.plot(
                coords[0],
                coords[1],
                c=synapse_col,
                **synapse_plot_kwargs,
            )
            ax.scatter(
                post_coord[dims_np[0]],
                post_coord[dims_np[1]],
                c=synapse_col,
                **synapse_scatter_kwargs,
            )
    else:
        raise ValueError("detail must be in {full, point}.")

    return ax